P1309 code & OD stuck on, after engine/trans swap to OBDII OS | Ford Explorer Forums - Serious Explorations

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P1309 code & OD stuck on, after engine/trans swap to OBDII OS


It's Always Something!
Staff member
Elite Explorer
August 1, 2008
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City, State
Year, Model & Trim Level
94 & 95 XLT's
Could use some ideas on where to start and solving these issues.

Please keep in mind I am new to the 5.0L in these rigs, and have only dealt with Explorer 4.0L for the last 12 years. I need to learn the 5.0L, just like I did with the 4.0L .

Issues at hand are:
1) OD is stuck on at all times, and can't be turned off by the column switch. I have yet to see the OD/Off light on this rig since it has been returned.
2) 1st to 2nd is quick- 2nd to 3rd is very delayed- 3 to 4 is also very quick.
3) Passing kickdown happens at less than 1/4 throttle, and instantly drops 2 gears, and RPM's hit 4k almost every time.
4) It has had a P1309 code since return as well. Only sharing this here, in case it is related somehow. I do not know if the CMP was removed & reinstalled during the engine swap or not. I also do not know if it needs removed when the lower intake is removed or not, but it was for a new gasket.

First a backstory to set the stage.
The rig is a highly modified 95 Ex XLT 4wd.

It recently had an engine & trans swap, from OBDI 4.0 to OBDII 5.0. I did not do the swap, and hired someone out of state to perform this, as I didn't have the knowledge, patience, or time to perform the OBD conversion. I do know some stuff, not a complete newb, and can comprehend most, but with electrical, it's best to talk in simpleton terms. :D

The previous setup:
97 4.0L OHV. Only lower end was used, and everything else was the stock 95 components.
95 manual ECM w/engine harness repined for trans harness
M5R1 4wd trans with custom harness
Atlas II 4.3 Transfer case w/VSS signal output convertor
8.8 Rear-D35 CAD front, w/manual switched shift fork actuator (on/off/on)
ABS delete (light on in dash pod)

The swap setup from a 98 Mounty donor:
98 5.0L w/3 wire CMP
98 Auto ECM
98 engine & trans harness customized by installer. What was integrated to the 95's is unknown by me.
98 4r70w rebuilt trans
98 GEM & 98 shifter w/OD switch
98 dash cluster w/ABS bulb removed
Atlas II 4.3 T-case (VSS removed and plug installed)
8.8 rear with OSS/ABS sensor- D35 CAD front w/manual switched Shift fork ( Wired wrong, not presently working)

I asked the installer for a new wiring diagram showing what was done, so I can figure circuits in the future if ever needed. I only got a diagram for Aux items, but nothing for the engine/trans harness, so there is no help from them with this, and the reason I am asking for your help now.

I do own an SCT3 3015, and can use it if that helps any? I have yet to plug it in, as I was told not too, with a CEL on. I want to believe that is only for loading a tune. Can't I use it to see whats going on with the ECM as is? I'm also new to this tool as well, and might need guidance with procedures for something like this. (dang newbs)

Thanks for any insights, tips, knowledge, guidance, or advice in advance!


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I have not done a swap myself, so I will be reading thru other threads and trying to help this way.
My sister is in town, so i wont be able to start looking at details and ask you to confirm things till probably end of next week. I'm sure we can get thru this, as it sure sounds like the trans connector pin out is not quite right. I'm also really wondering about that cam position sensor.....I thought the 98 pcm used a 2 wire, and not the 3. I'll have to dig in to this.

@vroomzoomboom might have some insight also.

i will say the cam sensor shouldnt effect the trans, or it didnt with me. the flag was smashed off it and the spinny thingy was bent to hell, but it still ran and shifted. just tossed the check engine light. if you have what sounds like a belt chirp, chances are its done. or remove the cap on it and check it out. they are pretty easy to remove. 2 bolts (which i can remember the size, but can find out for you) pull the cap. it will be very apparent if its damaged.


same on the flag. if they are damaged, DO NOT buy dorman. buy motocraft for both the sensor and body, but i am sure you know this already.

now as for the trans part of it
maybe pull the column down and see if the shifter is unplugged or the wires going to it are damaged. quickest and easiest way if you ask me. it might be something that simple.
is the fluid burnt, or stink like its burnt? was the fuild changed went the swap was made? how many miles on the donor? does it delay, or flare?
as for kick down, this one is a mystery to me, but i will throw things at the wall and see if they stick. older vehicles had a cable or linkage you could adjust. what comes to mind is a friends old 91 firebird he had back in the day. you would ratchet a cable up by the throttlebody, and would make everything happy again. these dont. this is a long shot (very long shot) but doest the tps also control how the trans shifts? look at your voltages and see what they are with ignition on. you should be something around .98 volts at idle, and 4.5 if i recall at wot. after that, its grab every harness and give them a good shake, or pull them off, use electrical cleaner on them, make sure no pins are bent, and put them back on and see what happens.
i know you know most of this, but like i do sometimes is over think things and not go for the easy stuff first

bolts are either 7/32 or a 5.5mm. also, like jon said, 3 wire. just looked at evil, and thats what it has.

It's a 3 wire. I made sure before I made the post. It's not making any noise at all. That 1309 code says it is related to the CMP timing, so it might need to be aligned? I do not have the tool for it. Rockauto has one tho. :( I would only get the Motorcraft, as I have already read about the aftermarket fails.

With the OD working full time, the switch in the shifter is making a circuit. The problem with not being able to turn it off, is either the switch is busted in the ON position, or somewhere else, after the switch. This issue really bugs me bad. I have to be able to turn it off, as this swap was entirely done to be able to tow a trailer. If it cant tow a trailer because of no control over the TC, this rig is useless to me now.

Trans was completely rebuilt after pulled from the donor and installed into the rig. All swap parts had 112k miles on them when pulled. The pictures I seen, looked like it had 212k on it, and never had a bath tho. It was extremely grimed up and filthy.

I was told the engine got all new front and top end gaskets, except the heads was not removed. The parts that I can see, I can see new gaskets on.

Hard to explain the shift points, but here goes....The time between shifts are different. When I say delayed, I mean having the throttle held at the same point thru all gears, from a stop or getting up to speed entering a Hwy, then as it goes thru the gears, 1-2 shifts are quick, as in it doesn't let the rpms climb, then 2-3 it takes forever, as it is now letting the rpms climb way too high before it will shift, then 3-4 is a quick shift, and barely stays in 3rd at all before it shifts to 4th. To me a flare is when it feels like it slips (like depressing the clutch on a manual) and rpms rocket before it will shift. I need to take a video of the tach as this goes thru the gears, so you can see what I mean.

I have already gone thru and wiggled the connectors, or at least the ones I can see, and no changes. I have not unplugged any to inspect the pins tho. I guess I need to spend some time with that.

Your right about the TPS Tim. I will get the meter on it. I had to adjust the old one on the 4.0 to get the voltage right, and know how to modify it, if it's off.

I wonder if the ECM was programmed correctly when they did it for the speedo? Will the tuner be able to see whats up with a download?

so for the tool, what i have done in the past when i was in a pinch, was go to the parts store, BUY a dorman one because it comes with the tool, go home, use the tool to align the snychro that i was using, box it back up and return everything. dirty move, i know, but hey, ya gotta do what ya gotta do!
what you have described is a flare when shifting from 2-3. if it was just rebuilt you might just have to have the bands adjusted, after that......well, lets just hope it just needs a band adjustment.

I will just get the tool from RockAuto.

I don't think it's a flare. It's not slipping, just takes too long to shift, and still pulls until the rpms are higher, like I have my foot in it. I will get video tomorrow.

Get rid of the 1309 code first, pretty dang easy on the 5.0 to align the CPS (cam pos sensor) only have to remove the coil pack for easy access
Bring Cyl 1 at TDC on compression stroke then check mark on crank damper, drop in cam sensor, make sure it matches picture and cinch it down. It can only really go one way since the teeth on the gear will only mesh in like 15 degree increments, so its hard to not get it correct.

There are several, and I mean several wiring changes at the C115 42 pin plug between 1995 and 1998 I am hoping the mechanic at least compared the 95 harness to the 98 harness at this plug and made required changes.

The trans was rebuilt. By whom?
I have seen about 10 column shifters with broken OD wires inside them, or the wire stretches in teh column where it tilts. For you I suggest you unplug the column shifter from the two wire plug behind the knee guard and do some testing. We want to see that OD light on the dash because if it goes into limp mode it will tell you.

I will assume since its running the 98 PCM came with the PATS key and the 98 dash also has the PATS stuff installed?

I would be happy to look at this rig if its anywhere near North Idaho :)

Thanks 410,

The trans was rebuilt by the 5.0 swap shops trans vendor. I asked for that vendors info, so I could get a warranty and if anything arises, I could contact them. All they sent was invoices for parts they purchased, nothing else. This leads me to believe it was a friend who rebuilt it, not a shop, and no warranty is given. On a side note... I did pay them to install a Transgo shift kit, but never got invoiced for the work or the parts, and it didn't feel like it was installed upon initial testing. I have managed to put a couple hundred miles on it (over 6 months), and with more use, and more variables in driving, the shifts seem to have firmed up. Now, you got me thinking about the limp mode, and no dash light to see it, if triggered,

I had a bad switch with a broken wire in this rig when I got it, and it was still auto. Dash light was on. Replaced switch, dash light went off when activated, and TC now worked, and allowed lockup. With that said, this new 98 shifter installed (went from manual back to auto again), the light isn't on, and OD is always on. To me, that says the switch is making a circuit, and the wires are good. Now, it might be the button itself is physically broken. I will unplug it, and see if it triggers the dash light or not. That's a good idea, and a place to start.

Yes, the Pats system was installed, with new locks and new keys, that work.

I am only about 1500 miles away from Idaho. lol (Thought you was in CO? )

Vroomzoomboom, your right!
I am familiar with the shift kits, as I have installed them myself in the past, back in my hot rod days. Those had way more HP, and less weight, and the "Tire Scratch" from shifting was extremely aggressive, and jarring to the point it would kick the ass out to the right a tad, and leave rubber on the pavement.

I am in no way or in that frame of mind that this rig could or would ever be that aggressive with the shift kit. This low HP, heavy beast turning aggressive 35" off road tires, will never ever see that kind of reaction as is. I do think it would at least kick me back in the seat a little when shifting, with a stage 2 kit, which is what I asked for.

If they did install it, all it would take is a single spring mistake or a single hole drilled wrong to cause these issues. I just can't say, as I never got an answer, when I asked if they installed it or not.

The unknown variables that happened with this swap, is what is making this so hard to figure out. I have to start somewhere, and this thread is the first attempt to get this rig fixed.

Sorry for the long winded posts, but I am attempting to give as much info as possible to help you guys understand better. Please keep asking away!

When I get a chance I will correct my error, and disconnect the OD switch again, then take it for a spin, and see if it is still on or if it is off. Rather do that, than rip the cluster out.

Only made time today to get that switch disconnected. Been working on the house all weekend. I need a clone or two to keep up with everything!

Had a chance this afternoon to look at the cmp sensor. It was easier for me to lift the coil packs, to get to the sensor screws, then to fight getting at them as is.

I quickly discovered it was missing a nut for the coil bracket, so only had 3 to remove. (sarcasm)

I then quickly discovered that the left coil packs pin connector moves up & down by 1/4", and feels like it's broken. (disgust)

left coil connector.jpg

After removing the sensor, I found rust inside from one screw, and rust on the Sync head. I don't see anything broken, or bent.

CMP sensor.jpg

95 cmp.jpg

Here is what I don't know...

Isn't there supposed to be a tiny flag coming up from the sync? I don't see one, just the half round metal shown here.

Is it normal for water to get in from the screw? I don't see how that can happen, unless it was under water, or left out in the rains after being pulled from the donor.

What say the masses about all this? Good, bad, or just ugly?

I do know that this engine was badly rusted when pulled from the donor, and they rattle canned flat black on the engine, and silver on the intake to try to clean it up. I can already see the rust coming thru now. Wondering now, if this donor was in the hurricane floods, as it was bought directly after all that happened in TX. Just thinking aloud here. One would think to clean each and every part before being put back on, but that means you have to care a little. (more sarcasm)

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The half circle metal is the flag.
Clean the cavity out real good, blow it with some air after, and throw your new sensor ( cap only) on there. I'd also replace the coil pack with loose connector, this could be the whole issue.