OK, I figured out what the capacitors were once I took a look at the engine bay. They are the single wire connector pieces mounted on the front of the head.
Anyway, I have the following
* Key off ground resistance from battery post to pin 15 on ccrm is 1.7 ohms
* Key on voltage at capacitors was 12.8
* Fuse 2.21 has 12 volts on both sides
* On the ccrm you asked for voltage numbers on pins 23 and 5. However pin 23 was the a/c coil, so I assumed it may have been a typo instead of pin 24. Anyway, 5 and "24" had 12.8 volts
And to answer your question, no the engine has never ran since the engine swap. We just swapped the motor in on new years eve. I have been chasing this issue every since. But as I mentioned early in the thread, the pcm used to communicate with my scanner, the theft light would go out before and during crankin and the cluster used to work. Now midways thru lookin for why the car had no fuel, and appeared to have no spark, it seems as thought the pcm went down also.
As for rodents, that was the first thing I looked for. The only sign of damage I have seen is some nesting on top of the fuel tank. But the rest of the car looks good and the wiring on top the fuel tank looks good. I have also tried disconnecting the fuel tank connector harness to eliminate it from the wiring in case any of it was shorting out. And you are correct, the ccrm has stopped making the clicking noise.
I will go back out and recheck my connections over by the battery again. I had checked them once before when all the problems began and didn't see anything wrong. I am also going to study the connector diagram you attached and check back shortly