dont suppose you checked the compression on each bore before you removed the head? it is a possibility that the overheating issue was nothing to do with the problem areas you are finding now, but it may have caused them (thats head gasket damage and overheating, not cracks). i dont think you need to worry about the cracks on the block, as long as the liners are ok. The overheating could have warped the head, thus creating a leak path for the coolant to a chambre, or something along those lines. Also, i dont think your high rev missfire would be related to this, but if it is missing on idle, sounds like its running on 3 cylinders or something, this would probably be the cause.