So I finally had my codes pulled today...
Intake air temp sensor voltage high
coolant temp sensor voltage high (two wire)
#1 fuel injector improper fire
fan relay circuit fault
alternator field circuit fault
The last two codes are a result of the swap. The fan relay code will be gone once I convert to an electric fan and wire it into that relay. The alternator fault is because the alternator used on the 4.0 is computer controlled, it kicks on when the computer tells it to, and the only way to fix that is to swap to a 4.0 alternator, which I will not be doing.
The other three codes, however, must be addressed, as the coolant temp sensor and air intake sensor play a huge part in the computer's ability to properly tune fuel trim. The fuel injector fault also obviously needs to be addressed, as it could mean a lean condition in that cylinder. I will make sure to edit the EFI swap writeup to include the two codes mentioned in the above paragraph.
The first three are probably the most major and primary cause of my engine vibration, and the awesome part is electrical can be a little tricky to diagnose, but parts are FAR cheaper to replace than major engine components, and the problem can be pinpointed, proven, and fixed (this is why I LOVE efi, and why carburetors are obsolete). I have two spare unused injectors, as I bought a set of eight when I initially upgraded them. So, I just need to break out the multimeter and see what I can find....
First though, I'm going to replace the parts on my front end tonight, it's supposed to snow and I'd rather not have snow and slush dripping on me with the car in the air...