Ok, I have pulled the fuel pressure regulator vacuum line off an no fuel is coming out. It didn't seem to have any impact on how the engine was running either. I probably need to go back through and double check all of my vacuum lines though, because I did have to redo some of the plumbing. Shortly after the engine swap, the ring gear in the D-35 rear end got a bad case of gingivitis and lost a few teeth... so I replaced the rear with a C8.25 from an automatic (for the better gear ratio and strength) and the front with a non-disconnect D-30 (to match the rear gear ratio and get rid of the POS vacuum disconnect axle). It's possible I may have missed a vacuum line somewhere.

As far as the temp sensor, it would make sense how having the sensor reading from the thermostat housing could affect the mixture. I remember when we were putting this all back together and I tried to get the plug out of the block and failed. If memory serves me correctly, we broke off a 3/8" breaker bar tip in there and it wouldn't budge. I might need to give that another go and see if I can get it out.

I haven't been able to check the oxygen sensor, but it's likely the original sensor that was installed on the Jeep from the factory. However, I've seen O2 sensors go bad before, but never cause an engine to run THAT rich. I'm not gonna rule it out as a contributing factor just yet, though.

And in regards to the intake ports not lining up because of the difference in port height between the 90 and 96 heads, I did notice that. However, it was a very small difference and I wasn't too terribly concerned with it. It actually ran freaking awesome when we first got it running. And the last time I changed the plugs, it was accelerating better than it ever did before the swap, just having the dying issue.

So, it looks like I need to look at relocating the temp sensor back to the original location, check fuel pressure, check the O2 sensor and double check the vacuum system. Now, if I could just get a day or two off work to do all of this...

I appreciate the input, guys, and I'll let ya know what I find out.