Wiring harness rubbing? That's under the tank. Get some split plastic tubing at a auto parts store or at Harbor Freight and wrap it around the wires. Has worked on mine for years.
I used electrical tape and wrapped all the wires....
BTW

railhed1
Regarding the bolts, they just need to be torqued correctly and turn signals, never had a problem....
Just buy a Clymer Manual, it will save you alot of dough, plus watch alot of youtube videos, search for KLR 650 and grab some popcorn....