If your rectifier has 5 wires it's not stock. but it could work if the circuit I referred to is internal . I think  rewiring the bike would have been enough of a job to begin with ,but changing from the stock components was your downfall, the fact that their mismatched leads to damage (like your pickup coil).

The pick up coil is not damage, the connection was weak... Now fix.

Thanks for the suggestions and constructive criticism.

I didn't create the poll... I guess is a different model than yours, the rectifier has only 5 wires, what can I tell you?

I misspoke when I call it CDI, in fact it's a stock TDI I purchased online matching the part number on the original.

OK ! I was wrong,( well half wrong) I've found out that there are two kinds of regulator/rectifiers  5 and 6 wire, depending on model of the bike . Both have 3 yellows, one red, one black ,and some have an added orange/brown wire(mine) the latest stock number listed is 32800-24 B11 but I haven't seen a pic.  to determine which it may be. The wiring diagrams I've seen ,even the one in the Tech section ,shows a 6 wire and that is from a 2009 bike, very confusing! Dave you said you have a 5 wire from a 95 ,I have a six wire on a 95 (P), was you bike a CA model, or other than a P ?