wouldn't an overcharging situation blow fuses before wiping out the ecu ?
You are not the first one to have an over charging R/R. There were a whole rash of them 3-4 years ago when they were selling the $39.95 "kit" on Ebay with and R/R, stator and gasket. The Chinese R/Rs seemed to be the only ones that failed this way. Others just stop charging or go out in a puff of smoke, short out and blow the main fuse.
The first symptom is usually the headlight or other bulbs keep failing. When the battery gets low on fluid due to overcharge, the next symptom is the smell of rotten eggs. Last as the battery boils out, the voltage spikes and takes out the electronics. (the battery will act as a voltage "shock absorber" as long as it can)
The classic ECM failure is that the fuel pump will not prime or run as well as the display showing "CHEC" which means the ECM is not talking to the cluster.
Since you are able to display fault codes, that means the ECM is working and sending data so that is a good sign. Unfortunately, having that code, along with the overvolt history makes it hard to pinpoint which is bad.
That is why I suggested you find a local rider with an 08 or 09 600 or 750 that will let you plug your ECM into and see if it runs fine. I've never done it, but I wonder if an ECM flash service could also check for proper operation?