I have a 96 civic EX manual.

I swapped the engine and put a a 96 civic LX engine in.

I switched the wireing harness and computer

Engine idles at about 1600 rpms

For the first few minutes of starting the car when its cold it runs good but after a few minutes it starts studdering when excelerating.

could it be in limp mode? or timed wrong or something please let me know what it could be and how I could fix it thanks