I have same issue
I have same exact issue with my 2001 honda civic ex. I swapped engine, fuel pump sounded when in on position, fuel in fuel rails, engine ran normally.
I don't remember how many ground wires they are. I know I have battery ground to body to transition on. I also have short thermostat ground wire that goes to wire harness. And I have ground from thermostat to frame above radiator. Are there any other grounds I am missing?
So I tried starting up car after I swapped engine, Drive light blinks 2x and then goes out. Engine turns, but doesn't't start. I don't hear fuel pump. I pulled fuel rail hose off, no fuel. I then checked for spark, no spark.
Then, I thought it could be the ECU. So I just pulled ecu out and looked at the board and it looks normal, nothing burned or melted. I made an offer for $50 to buy it, I hope he doesn't accept my offer now seeing the ecu is fine.
If someone could show me picture of where the grounds are? I am lost for what to do next.