I appreciate your mechanical/machinist abilities. Porting is a real science. If you really want to learn about it, start with a search...not just on this website but using a general search engine.
Regarding your question about removing material from the face of the cylinder and/or head, I believe this could help your overall power and decrease chances of detonation by providing proper squish clearance, assuming clearance is currently greater than ideal and the machine work was done properly. However, the downside is that as you increase compression you will actually reduce high rpm power, particularly if the proper other porting modifications aren't done at the same time. Many times the are inside the squish band is machined a bit to bring the compression back proper. Also, if you make squish clearance too tight you will crash the engine. Really, I am oversimplifying here and again I think you will find a world of knowldege by searching.