To reset the ECU you either remove the EFI #1 fuse for 10 secs or disconnect the battery for 30 secs (Just disconnecting the negative terminal works fine)
The battery should ALWAYS be disconnected when working on the wiring, especially the ECU wiring. Cutting and joining live ECU wires is a very bad idea. It's unlikely to have damaged the ECU but I wouldn't be amazed if it had.
Anyway, the simplest way to diagnose whether the FCD is causing you problems is to disconnect it and put the wiring back to stock. If the problem goes away you know that either the FCD is faulty or the fitting of it is not sound.
Also a fairly common issue with FCDs is that they need a really good earth. You may solve your problems by earthing it to a chassis point rather than to the ECU Ground wire. The bolt that secures the ECU cover works well as a grounding point.