If the crank and crankcase is still good than rebuilding the top end is a easy DIY and it doesn't cost a lot and you don't need to pull the engine to do it.
If the crank is bad than pull the engine and tear the top end down and send the bottom end to a machine shop for repairs. New jugs and pistons and a set of used heads won't cost you a lot. If you are lucky your jugs can be punch to a 95 inch or .010 over which ever works for you and heads can be reconditioned. I had my stock heads reconditioned at the local auto machine shop for $50 each, I had to provide the valve seals. The auto machine shop will bore the jugs too.
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08 FLTR candy red sunglo,with 2015 103 HO, V&H Dresser Duals with Monster Rounds, Power Vision tuner, Willy Shiny Wheels and Forks and a bunch of other stuff.