Completely LOST!

Sorry if I'm in the wrong place, never done anything like this before. please bare with me.
Little back story to my Truck.(2000 Mountaineer 4.0L SOHC)
I got the truck with a blown motor (blown head gasket, milk shake oil mix).
Installed a quite junk yard motor, upon install put new upper and lower intake gasket rings on. Truck ran perfect, but you could hear a vacuum leak. At the time I was working a repair shop so we all tinkered around with it. It seemed like the fuel pressure regulator was dead. Replaced it, no change. Everything I read online kept pointing to bad intake rings. Grabbed a set on my way home from work and changed them, not thinking at the time the motor was still hot. replaced the gaskets and while going back together I found the vacuum leak. the twin breather lines that go to the canister under the drivers headlight (or there abouts). Put the line in fully this time, must have half azzed it the first time. The problem is, since then I have 3 DTC's and a rough idle that I can't seem to rectify. If I pull 4,5,or 6 plug wires very little to no change in idle, if I pull 1,2,or 3 the engine stalls out. Wires are only removed one at a time and replaced before trying the next one.
First code P0171 Bank 1 Lean
2nd code P0305 Misfire Cyl 5
3rd code P0306 Misfire Cyl6
I have gone through 2 sets of intake gaskets
pcv valve hoses
mass air flow sensor
switching the o2's
I have done a full chain and guide set replacement
thinking I may have warped the intake upper or lower while taking it apart hot replaced those too.
new plugs
new fuel filter
both cyl 5 and 6 show about 75 psi on compression test if done per Haynes manual extended crank I can get it up to 120 psi on both cyl.
during the Timing Chain Adventure during reassembly I found 1 half of a valve lock in the oil pan. the lock was missing from cyl6 rear most valve.(I don't remember if that is intake or exh.
Any insight would be helpful.

did you check to see if you cracked the intake? you might have maybe if you over tightened the bolts. it is plastic after all.

Thought about it, but both of them? I wouldn't think so. I'm using 1/4 drive hand sockets and ratchets.

I'm at fault here.
The three DTC's listed have been constant since pulling the intake after replacing the fuel pressure reg.
Any combination of old and new upper and lower intakes makes no change in idle or tripping CEL. Timing chain replacement didn't change anything either.
There was zero plastic on any of the guides at the time of replacement of the chains and guides.

low compression

120 psi is low for the SOHC V6. Was the throttle plate wide open when you took the readings? How does the compression for cylinder 5 and 6 compare to cylinder 4 and the other cylinders?

Did you use the OTC 6488 timing tool kit to time the camshafts after replacing the cassettes?

Yes I used the otc 4.0l cam tool kit.
Cyl 4 at about 155 psi, never checked the right bank.
Again all idle and CEL conditions existed prior to the cassette replacement.
What has me concerned is that 1 half of a valve keep (lock) found in the oil pan. I can't figure out how it got free from the valve stem.

interference?

The compression is low on all cylinders in bank 2. When I perform a compression test I tie the throttle plate wide open, disable the ignition, and crank the starter for 5 compressions of the cylinder under test.

So you installed a "quiet" salvage yard engine but then replaced all of the camshaft timing components? Why? Did timing chain rattle develop after the engine was installed?

Is it possible the bank 2 timing chain slipped enough for piston to valve collision? If so, it may have been just enough to dislodge the valve keeper. Minor collision normally results in exhaust valve to piston collision.

I suggest that you test a cylinder in bank 1 for comparison. The compression should be about 180 psi.

What is your fuel pressure? Low fuel pressure can result in a lean condition and misfires.

Yes the guides did degrade after about a year, that's why I went after the cassettes. I will take bank one comp tests tomorrow along with fuel pressure. The 5 revolution test is what gives 75 psi let it go more and it can build more psi. A impact of valve to piston is possible I'd imagine, that's the only thing that I can see giving the keep the ability to get off the stem.

This is as far as I got this morning. Fuel pressure 60 psi. Cyl 1 compression 150psi motor was too hot. Will get the other 2 done asap.

low compression

I'm concerned about your low compression. Are you sure that you timed the camshafts correctly using the tool kit? If you PM me your email address I'll send you a copy of the engine assembly instructions with diagrams showing the use of the tool kit items. If you review the instructions you can confirm you did everything correctly or maybe identify something you missed. Do you know how many miles are on the salvage engine?

90,100 miles is what the donor odometer displayed. I'm more than certain that the cams balance jack and crank were lined up. The cams gave cuts/gaps that are off center preventing mis-orientation. Between download loaded pics from this site and the Haynes manual and breaker bar rotation while on the stand I'm 99.9% sure I'm in time. Cyl 2 125 psi. Cyl 3 not able to check as the Guage I own doesn't clear the HVAC box. Only other thing I can think of other than collision is weak valve springs, ie can't rebound fast enough, and is why I can get 125 on extended cranks. All symptoms existed prior to chain replacement.

prior symptoms

Did you happen to check the compression prior to replacing the timing chain components? 125 psi is low for an engine with less than 100K miles. Had the engine been sitting (not running) for years? Maybe the cylinder walls and compression rings rusted. The Volvo Turbo Wagon I purchased had set for about 18 months because a mechanic couldn't fix it for the previous owner. The compression was very low when the tow truck delivered it. I was afraid the head gasket was blown. I pulled all of the plugs and inserted a small amount of Sea Foam in each cylinder. The next day I checked the compression and then added more Sea Foam. After doing that for 5 days the compression was up to normal.

Are you measure the compression with the throttle plate wide open?

Low compression could be due to weak valve springs, burned/worn valves, incorrect valve timing, worn compression rings, cracked heads or blown head gaskets. According to your posted readings:

cyl psi
1 150
2 125
3 ?
4 155
5 75
6 75

The above indicate a worn engine with a blown head gasket or a cracked head affecting cylinders 5 & 6. Did the engine happen to overheat due to air in the block after replacing the timing chains? The SOHC V6 requires care to prevent overheating after a rebuild. I leave the thermostat out and fill the block with coolant to that level. Then I install the thermostat and housing, the upper radiator hose and fill the radiator but leave the cap loose to let air bubbles escape until the engine has warmed up. Then I top off the radiator, install the cap and fill the coolant reservoir to the normal level. The engine overheats very quickly when the water pump is only pumping air and the engine temperature looks normal because the sensor has no contact with coolant.

I don't know how long it sat prior to being removed. I did watch the removal to insure that I didn't get the bait and switch. Never over heated while in my possession. I know some old timers that squirt machining oil in to cyl's to see if compression comes up. After the initial swap the engine ran trouble free for about 10 weeks. The developed a vacuum leak as stated before. After upper intake reassembly it has not run smoothly.

EGR tube O ring?

Did you replace the EGR tube O ring when you replaced the upper and lower intake manifold gaskets?

It becomes brittle from the heat and is often damaged when the upper intake manifold is removed or installed.

Did it twice at the time of the swap and the chain replacement.