The harness & ecu should be working fine.

1. Is the car throwing any codes or is the MIL light on ?
2. What codes is the vehicle throwing ?
3. Did you check the spark plugs to see if they are fouled ?
4. Did you examine the firing order / plug wire order, I have personally seen the chiltons or other cheap manuals be wrong for an integra (firing order list).
5. Was the engine running in another vehicle before ?

There are a lot of variables to look at without seeing a vehicle in person.