Hello guys! I just wrapped up a swap on my auto 2000 Honda Accord, no sunroof but power windows (EX??). I swapped out my f23a4 paired with an auto trans for a jdm f23a1 and a jdm m2a4 trans. Everything is all complete, plumbing, on-the-motor/trans wiring and now i'm having trouble getting it started .... Fuel relay plug is getting 12 volts to two pins, not sure how many need power, but the fuel pump itself never kicks on, nor can I hear a click under the dash. Secondly One of the main plugs (big grey one) that goes behind the shock tower doesn't align with that of the new harness off the motor..

 

Go to any of the online Honda dealer parts departments and punch in your VIN, it will show you what model you have.
Most likely an LX or SE.
JDM harness' have different plugs and sometimes not all the same number of circuits as USDM.
MT and AT will have slight differences in harness.
A1 engine harness will be slightly diffrerent than A4.
Combine all three, and probably a year or model difference, and you get mixed plugs.
I'd suggest reusing your A4 engine harness and modify it to work on the A1 engine so it fits your existing fuse box and vehicle wire harness.
Or locate a A1/MT harness for your year car.

A4 SULEV cars are a bit unique in several factors, not just power/drivetrain but exhaust as well. Not really the easiest variant of Accord to modify.