Actually the charging system is fairly easy to troubleshoot. It's either the stator, r/r or the wire connection between them. He didn't say anything about checking or replacing the stator.Sounds like you have a lot going on and it must be confusing. Look at the fault finding guide on this page and see if it helps sort things out.
How to Diagnose Electrical System Issues on Motorcycles Any well-working modern motorcycle charging system will produce a voltage over the battery terminals in between 13.5V DC and 14.5V DC, over the entire rev range. When you suspect a fault in the system, this is the first thing to check on...www.electrosport.com