Rep Power: 0

I recently bought a 97 civic EX coupe so I could swap my recently rebuilt D16y7 into it. It came with a Y8, but it didn’t run. I swapped the Ecu with the one that was originally with the Y7 and I also swapped the engine harness. Is there any reason it won’t start? It sounds like the fuel pump won’t turn off when I put the key in and it just doesn’t want to fully turn over.

 
Rep Power: 222

Put it back to normal, make it run, then worry about swapping stuff around. You've introduced way too many variables.
pump relay may be stuck if it keeps running without the key
slow crank might be bad battery, starter, connection, partially seized engine, or something seized on the belt drive.

 
Rep Power: 0

Would the Y8 Ecu and Y8 engine harness work with the Y7 motor? I had it on there before swapping to the Y7 ECU and engine harness and it ran but there were some plugs that didn’t have any connections on the Y7 motor

 
Rep Power: 126

That's because you're putting VTEC components on a vehicle with no VTEC. It should in theory run as well as the Y7 it's supposed to be, but you'll get fault codes for the obviously missing parts.