my lil brother just got an 88' lt250r.it just got an engine rbuild.it is very hard to start and dosnt run very good.it has a penny sized hole about an inch from where the head pipe meats the engine.could that be affecting it?

 

The hole in the head pipe will definitely affect the performance of the bike,replace the exhaust(unless you know someone who can repair it)and go from there. Also from 87 up models have a powervalve on them,make sure thats working correctly,do a compression check,sounds like it may be low.