When using cylinder shims to achieve the proper deck height /compression ratio, do I leave in the thin original shim/aluminum gasket or does the new shim take the place of that?

Kinda depends on how much height you need.

The Cap'n

I really need .016 but the only shims I could get were .010 and .020.

So would it be ok to remove the standard shim and just run the .020?

I guess what I am asking is can the thicker deck height shims replace the standard or do you still need to use the standard for sealing purposes?

You can use up to 3 shims, I'd run the .010 and the standard which IIRC is about .008.

Only place I used to use RTV is under those shims, some use curil derko (basically same as RTV) or threebond.