Im sure youve checked this before but.. when ever i suspect more than one electrical fault on a bike i head stright for the earths. I know youve been thought most of the harness but just have a look at the engine earth and the colour of the main earth lead. If the one wire you replaced to the PGM was green then there's a good chance theres some others. A bad earth will cause hell on a bike.
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If I have to take the carbs off once more...