Welcome. With the number of issues you have, it is best to start your own thread rather than reviving a 10 year old one.I took my 2002 GSXR 1000 in to K's Motorsports in humble Texas & I was pulling up c-46 code for the exhaust actuator valve due to putting an aftermarket shorty exhaust on and taking factory exhaust system off. Which I knew that it was causing the light to come on, but after they put the servo buddy on my bike "the tech traces down a wire going to my that was cut and told me he had to solder it back together which cost me ½ hour!" Could this be the wire that you're talking about needing cut? With the only exception being that I was still getting the FI46 code when put in dealers mode!!! Since I've got the bike back from the shop, I've had more problems than what it actually went with and it seems like it's getting worse like over charging my battery causing my bike to bog down more ( while not being in a load & under a load ). Which I knew the bike was bogging down but only under a load until it went over there. I know my TPS was adjusted correctly with the -C00 showing on cluster. They said they adjusted my TPS which was already set properly!!! If I can tell you the color of the wire tomorrow, is there any way that you may be able to tell me what it was for and if it was needed to be soldered together?
If I remember, it is the wire on pin 30 that is disconnected to stop the C46 code but you need to search and confirm that.
If that was the only wire cut at the ECM it is likely that wire. It is the only "fix" I've heard of that involves cutting or disconnecting a wire at the ECM.
If your bike is actually over charging the battery, you need to stop riding it and fix that before you cause more damage.