As for the pipe, I have an ATV sport article on Chad Lohr's open class duncan quad. He was using the PT race pipe and the PT eliminator on a 340cc engine. I don't know if that was a newer version of the eliminator though. You could call duncan and ask them if your pipe will work okay.
On a stock cylinder, lrd and others offered a 300 kit using a re-sleeve and a 72mm piston. That would be cheapest route. You could also get a new 310 kit which also uses a 72mm piston. Lastly you could use a smaller bore and a stroker crank and achieve 300cc. Call some different engine builders and get their thoughts. ESR likes to build strokers. Some builders don't.