Was running fine, then burned the CDI box, installed a new one, idled fine for 20 min. Gave it some throttle, the R and N light started flashing, back and forth, RNRNRN, then the new CDI box burned up, I'm completely lost, any ideas?

 

Probably the voltage regulator was overcharging and has slow cooked both CDIs. ALWAYS check the wiring to the CDI before fitting a new one. The earth wire must be earthed or it will blow the CDI. Then when you get the new CDI on and the bike running, first thing to do is check voltage across the battery, if it goes over 15v stop the engine and change the regulator or it will burn out the new CDI.

 

I wouldn't exactly call it a slow burn, it was very quick, fine until I gave it throttle, then pop.

 

I replaced the voltage regulator, and CDI, now the reverse and neutral light both stay on, I'm scared lol. Your thoughts?

 

Check the earth leads, on a Yam they can look fine but not be. May be time to get a manual and check the wiring using the diagram.

 

Did you check the charging voltage at idle after the new voltage reg was installed?

And for sure clean and check all grounds.

A multimeter and a manual will go along way on trouble shooting.

 

Yes it stayed just over between 13/13.7 volts