Quote Originally Posted by Main Stream
The problem you have is that you are running a bigger motor on the stock ecu. If you look at the fuel trims (OBD2 scanner with realtime data) you will see that the fuel trims are too high. This means that the ecu is seeing that the a/f ratio is lean and trying to add fuel. After a set time of the ecu seeing these high fuel trims it will throw a CEL for System too lean. The only easy way to fix this is too get a adjustable fuel pressure regulator and raise the fuel pressure until the fuel trims get between -10 and +10. You will need a scanner with realtime data to see this. You may be able to just take off the vac line going to the FPR and plug the line. This has worked on a customer car of ours that had a B20/vtec and had to get emissions with the stock B16 ecu. Good luck.

That is funny I have done this same swap same ecu with no issues!