I have a Polaris Trail boss 325 thats overcharging 17vdc when you rev it up and seems to hit a rev limiter at about 1/4 to 1/2 throttle. The factory reg/rectifier is discontinued. I ordered an cheap aftermarket and it did not fix the problem. Any ideas?

 

Odd. Its is entirely possible you got a bad new one and would not be the first time that has happened.
Do you know for a fact your battery is good? Over or Under charging could indicate a bad battery and yes both can affect the ignition.