I am in great need of assistance... I have an eclipse from hell!

Here's the gist of it... I bought it, swapped out the engine with a JDM 4g63T, including the wiring harness that came with the JDM engine... Mechanic calls me and says the starter wont work, so I give him my old one which i know works... Swaps it still nothing... I call the JDM dealer and he tells me that someone had a similar problem... So I get the mechanic to take the tranny out and change the flywheel since the Jap. one is smaller, that fixed the starter problem... Now to the big part...
After the installing the new harness, he is getting some error on the computer that one of the cables isnt sending some info or something (i would specify but im a noob at mechanicism), and he tells me that I have to find a specialist that works on just cables and stuff and test out each wire till the problem is found. Also, somethin about the CV joints in the back. If anyone has any info at all please help. Im goin to work in a little, and ill be speaking with the mechanic in person tomorrow so ill be able to give more info.
--TIA

Btw, I'm Josh, ^ 1st post in this forum