When i read text i saw so many repair attemps and thinking by repair people that i doubt many of them capability and understanding of what they are fixing.
As many have requested please get your bike running and measure what is voltage output bike is giving to battery with multimeter (voltage meter)? If reading is something between 14.2-14.5V then your bike rectifier is ok. if it is over 14.5 V or more likely over 15V then it is bad and your bike is burning your battery.
Paraller connection what you have done to your battery might be enough to hold overvoltage some time as you incread A/H to 18 amps and basicly you have two normal batteries there now(how much is normal in GS650? 9 Amps?) but it will fail eventually.
Try to print out or get this fault finding diagram, get multimeter and start to follow instructions and you should find reason quite soon.
https://www.electrosport.com/technic...ng-diagram.pdf
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