Also, all the harness connectors related to the donor motor were still connected to it, (it came with the intake attached)

 

You should use original 5-speed the PCM (ECU). Usign an automatic ECU on a MT vehicle will cause a check engine light to turn on. You kept the 5-speed transmission with the original VSS, right?

Have you checked for engine codes?

Did you verify the injector resistor bank is plugged into the correct connector?

You may be better off using the original harness that was in your car, because it would eliminate one of the variables that can cause a problem.

 

Were both engines the same trim level (i.e,: LX)?

This is more detail to add to some of what already was said by poorman212 and PAHonda:

Engine Harness ((L4) (DX, LX, Canada EX)
Connector Number of Cavities/Color Location Connects to Notes

C118 1-BLK Middle of engine Back-up light switch (+) M/T
C119 1-BLK Middle of engine Back-up light switch (–) M/T

C120 2-GRY Middle of engine Countershaft speed sensor A/T
C121 2-GRN Middle of engine Mainshaft speed sensor A/T
C122 3-GRY Middle of engine Shift control solenoid valve A/T
C123 2-GRY Middle of engine Lock-up control solenoid valve A/T
C128 6-GRY Right side of engine compartment Main wire harness A/T

 

Hey Redbull. Sorry about my very delayed reply, as I somehow missed your post and got distracted on my 'other thread, (no ecu light, no rev over 2800 rpms), which eventually became merged information. I will only be continuing on That thread as to Not cause any more possible confusion, lol. But, Will post my ultimate, total repair findings here once completed. Thank you much !

 

Everything is fixed and working correctly! Firstly, yes, you CAN swap a 1996 accord 2.2 motor from an automatic with it's harness into a same year, (I think a 1997 too), directly into a 5-spd. There will be a few extra unused connectors that can be taped off and stowed. The 'no rpms over 2800' ultimately was a bad Crank Sensor, which would not produce codes, initially. The 'no CEL light was do to a 'missing' bulb.

Thank you again!

Peace, Abundance and Joy,
Hondaddy