Finally, my first 360 and goals for it! I'll be asking a lot of questions.

Pretty much,^^^^^^^^^,.040" is safe. Just test fit the intake w/the gaskets You're using, You may have to trim the bottom of the intake bolt holes a little, & port match the
heads to the intake gasket esp. at the very top. Those are dished pistons, but they look shallow, You should cc them before taking that eng. apart.
Many just seal the end rails w/a fat bead of black RTV, it works.