I agree with maryland stang your compression would be around 10:1. As far as checking ptv clearance theres a couple ways. I think most people use modeling clay. Lay a strip or two across the piston where the valves would make contact, the strip should be about 1/4 in. thick, you can lightly cover the top of the piston and valves with oil so the clay wont stick to the valves and pistons. Make sure you put the cam in your gonna be running and also whatever else your swapping out if any. Your suppose to use a used head gasket when checking ptv clearance, but I imagine if you don't have one theres not much you can do about it. Put the head on your going to be using, put some bolts in the head, I think you only need to tighten them like 30lbs, then put your pushrods and rockers on the piston your testing, also your supposed to use solid lifters when checking ptv clearance. Once you have everything on the piston your testing turn the motor over a couple rotaions, if at somepoint it gets hard to turn over stop so you don't mess up the valves, once you have it turned over thru the compression and exhaust stroke pull the head, carefully remove the clay and check the thinnest area of the clay with a dial caliper intake should be .080" and exhaust .100". If something don't make sense go to
FORDMUSCLE webmagazine: Fundamentals - Checking Piston to Valve Clearance
hope this helps. Also if you can find out what cc your heads are after you milled them, this site will help for the comp. ratio. Stock the GT40 heads are 60cc I believe.
FORDMUSCLE.com webmagazine - Compression Calculator