In the process of replacing piston on 1989 Indy 500 Classic. Have everything dismantled but can't get cylinder off of crankcase. Anyone have any thoughts? Thanks in advance!

I assume you have removed the cylinder base nuts. It's possible that the base gasket is "sealing" the cylinder(s) to the case. You may need to encourage it to break loose with a soft rubber or plastic mallet. If your piston is stuck, that's another matter.