Also make sure you have a very good contacts at the 3 yellow wires plug. They tend to melt and over heat and take out the R/R if not.
Also make sure you mount the R/R to the stock location normally a piece of alumimum is there that transfers the heat away from th unit. I have seen lots of guys move them to a plastic mount or even leave them loose and then wonder why they keep going bad.
Do not charge a dead battery with your bike. Inother words if you ahve to jump start your bike take the battery off and use a charger not the bike to charge the battery. It over taxes the R/R.
Consider a larger heatsink Alumimum piece behind the R/R and or use a heat conductive liquid between them. (white stuff found between a transistor and heat sink) Can be bought at radio shack.
The fan is also a great idea. I had a F3 that would eat them and I installed a F4 R/R because it had a larger heatsink attached to it the F3 did not have any fins on the R/R.
Also make sure that new pipe is not putting more heat near the R/R. A lot of guys remove things like heat sheilds (sometimes a thick rubber mat) from there bikes cause they think its not for anything special. Its a heat sheild thats flexible. Be sure not to remove them.
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