There really isn't any way to estimate the compression on a setup like that without measurements/cc's/etc. The only way to get a so-so estimate is to do a compression check and see how it reads. Someone a long time ago posted a table that corresponded cylinder pressure to the engine's compression ratio.
Yes, flat top pistons will raise your compression quite nicely and much more than shaving the head or decking the block will get you. Stock pistons have a pretty deep dish to them, so flat tops would raise it quite a bit! Just make sure to size everything up if you're using a bigger camshaft than stock, you may need to cut valve reliefs in the pistons depending on how big the cam is, head gasket thicknkess, cylinder head shaved/block decked.
Bottom line, flat tops give higher compression which in turn creates more power and requires more expensive gas

I've heard the A series respond extremely well to higher compression, but I never experimented with it.