Like the title says, I just finished a 96 GSR swap into a 98 LS. I used a GSR engine harness but repined the engine bay connectors to that it is compatible with the LS chassis harnesses.

The car runs fine on the LS ECU, without any CEL codes, suggesting to me that the wiring is correct. However, something weird happens when I connect the GSR ECU. It runs fine for a little while, then throws a solid CEL after a minute or two (only when warmed up). After that, the car continues to run fine. I took it near redline once and both IAB and VTEC appeared to function.

I've visually inspected the engine, starter, and transmission grounds, and they look OK (although I have not continuity tested them).

Any ideas what's causing the CEL? Is it just that the ECU has gone bad while sitting on my shelf? I have a hunch that it's hanging up on one of the learning routines and then tossing the CEL.

Edit: everything is OBD2a

 

Its a solid check engine light when you pull the code? Did you pull the codes?

 

It's solid when I jump the service connector. I had my codes scanned today while I was having an alignment done, and the scanner indicated a no-connection for the knock sensor. I had no idea that would throw a code 0 with the service connector jumped. I will wire the knock sensor this evening and report back.

 

UPDATE:

It was the knock sensor. Apparently if it's unplugged it throws a code 0. I connected it yesterday, and problem solved. The car runs beautifully now.

I knew that the LS doesn't use a knock sensor, but my Helms did not show a missing wire in the engine wire harness connector, so I assumed it was pre-wired the way some Civics are. But it's not! So if anybody else has this problem, check the knock sensor wire.