even if the shop said the bottom end was fine, did you tell them that it had water and mud in the engine before they repaired the top end.
As far as a price to repair, you want really know untill you tear it down for inspection and clean it out.
The last one I rebuilt cost me alittle over $700 in just parts. New crank, crank bearings, timing chain, gks/seal kit, bore job and piston kit. I can't really say on a sale price, it's hard to get rid of a smoking bike.