Usualy the manufacturers make an engine case to be used by a variety of models. Same case different internals, its normal to see the liner not lining up perfectly with the cases, especialy on the exhaust side.
If you want to have a play with it get your dremmel out but dont go crying to anyone if you fuck it up
If you want more power/revs and there is room to raise the exhaust port height thats the way to go. But you will also need to look at opening up the inlet side of the crank.
Dont blame me if it ends up slower