crankcase, transfers, intake. most epoxies work fine in these areas. exh port is another matter
if it doesnt have a iron sleeve you can easily weld the roof lower. with sleeve im not sure if theres a filler material that can be welded to aluminum and iron simultaniously. could pull the sleeve out, weld the roof then install new sleeve with lower roof.
why do you think the roof needs to be 5mm lower ? i prefer to work in rotation degrees but 5mm sounds like alot in a short stroke engine