Well all, have some statuses to give. There's some good news, some bad news, and some potentially nasty news, so here goes.
The Good News
I got the Explorer all put back together and fired it up for the first time in over a month yesterday around 4:00 in the afternoon. Took about 2 cranks of the motor to start, stumbled a little and then fired right up. The pedal was a little slow to respond, but this seems normal when the computer has been reset (and mine was disconnected for over a month). Everything seemed to be pretty much ok on this front. After talking with a friend, he recommended starting the engine up for the first time with no coolant and running it for 1 - 2 minutes. He said that this will cause the motor and gaskets to expand and compress without risk of coolant seeping in if there is a small gap. After this all was good, so I let it cool down. I then filled it with coolant and burped the system (or so I thought).
After about 1/2 an hour or so, I fired the Explorer up again and everything still seemed ok. I let the engine idle for about 20 minutes looking for leaks, keeping an eye on the temperature, etc... Everything still looked fine, heater appeared to work, A/C was fine, all seemed ok.
Some Bad News
I then took it for a test drive around the block. As I got on it... low and behold, the miss at 4k is STILL there!
Now, the one thing I will mention, the spark plugs in the engine (despite only being 15k old) looked pretty nasty. It looks like oil from the valve seals were contaminating the plugs and possibly my ignition problem was causing them to get hot. This combination seemed to almost eat away at the plugs (I took a look at one electrode this time and it looked like it was about 1/2 worn already). My friend had told me to replace the plugs, but without a car, I was unable to get to the parts store to get new ones. I will be picking some up this week. This would also follow the previous problem I had with the plug wires causing a similar, but much worse problem (see earlier posts).
Some More Bad News, Maybe
After I got the Explorer all loaded back up, we headed out on the Freeway. Not 30 seconds after getting onto the freeway the Explorer started to overheat (Great). We pulled of at the next exit, I let the engine cool for a few minutes and then I pulled the radiator cap (letting it bleed off the steam into the resorvoir tank first). The water level was way down, so I started filling. The engine took about 1 1/2 more gallons of water and seemed to be happy. I then started it back up and continued on the freeway. Again, not 30 seconds or so and the temperature starting rising, although it didn't actually get to the "Hot" like it did the first time. I pulled off the freeway and decided to head back, leave the Explorer and deal with it next weekend because it was already almost 11:00 at night and we both were supposed to work today.
Now for what I checked. My first thought of course was "Great, Cylinder Head Gasket Leak". But, things haven't followed that pattern yet. The Explorer has not had steam coming out of its tail pipe at all yet, nor has the oil turned to a milky color at all. Similarly, after I took it for a test drive around the block, I left it idling in the driveway for nearly an hour and not an ounce of water spilled out (only a small amount of condensation from the A/C).
The overheating appeared to only occur once I got on the freeway. The other thing was, one the temp would start to rise, my heater would start to work, as soon as the temp dropped, my heater went cold. The cylce from hot to cold was almost instant (maybe 2 seconds from overheating to normal). Also, after putting in nearly 2 more gallons of water, it never actually got to the "Hot" spot, but only got 1/2 way between normal and hot. It seems like I just didn't get all the air out of the system.
I was basing how much water and time to let the engine burp based upon when I did coolant flush and Thermostat change about 2 months ago, but I didn't actually get all the water out of the block and the heater core that time, so that would certainly account for the additional air in the system and the weird heater issue. Plus, the fact that as soon as the thermostat appears to kick in, the temp immediately drops seems like air in the system.
One question on this front, I checked the Haynes manual and it said that the system should take between 12.8 and 15.7 Quarts to fill (+/- 15%). I've so far put in between 3 1/2 and 4 1/2 gallons (not 100% sure because I wasn't measuring my water out in gallons, just filling the system until it seemed full enough). How much water have those of you who have done things like this had to put in? I think I'm close, just a little concerned.
Some Other Good News and Notes
The new valve covers did clear the roller rockers fine with the removal of the oil baffle. The only spot that was close was in the corners at the top where I hadn't remove the casting material yet. They did fit, but if I pulled the valve covers to one side or the other, they would hit slightly. I opted to clean out the stuff in the corners just to be safe, but there did seem to be enough clearance for my roller rockers. That means, if you are running the FMS Roller Rockers which are clearanced around the sides more, you shouldn't have any problems at all.
I've also had the car running through at least 4 seperate drive cycles now, and there have been no CEL thrown yet (thank goodness). I will be throwing the OBD-II Scanner that Glacier let me borrow next weekend when everything else is together. I didn't have time this time because I got it all buttoned up just with time to leave... Biggest suggestion to anyone, don't rush, even if you've spent 30+ hours on it like I have (a lot of that is wasted time stumbling with getting 1 bolt in for 2 1/2 hours in 100* heat, haha). Also, a second pair of hands and eyes will save you a lot of time (took me about 30 minutes to find TDC on the compression stroke the first time because I kept passing it up).
It also looks like some TM Headers will be in my not too distant future (once I can resolve the miss). The drivers side header (which was replaced under warranty by Ford about 20k ago) was warped so badly that I couldn't get one bolt in. If I installed that bolt first, I couldn't get 3 - 4 in, even with a big breaker bar. If I put all the others in loosely, I couldn't get that one in. the Passengers side went on like butter, took 20 minutes. My guess is because of the wonky design of the drivers side, it just warped from heat. Time to start saving, haha.
The only other issue I had was with the egr. Because of the upper intake spacer and the taller Valve covers, I had a hard time getting the egr tube to clear and fit the EGR on. I ended up doing it, but the tube is sitting awfully close to the valve covers. I may force a breaker bar in there as well to "Adjust" the tube a little more.
I think that's pretty much it for now. I'll give you guys an updated as I find out more... a little bummed about the overheating, but glad that she started right up, that was probably my single biggest concern.