youll have to measure for pushrods, but theyre's a high probability that yes, youll need them. might as well check ptv clearance while youre theyre, just use an old gasket and bolt the head on (doesnt need to be torqued, just snugged up). a little oil on the piston and chamber, and the clay will lift right off. takes like 10 minutes to do, and since youll have to order pushrods AFTER you mock it all up anyway....
as far as milling, i wouldnt take more than the minimum to get them flat, assuming they even need milling at all, your machinist should be able to tell you.