I like to have a finger thickness at all potential contact points and this is fine with new or good rubber in the mounts. For clearance checking we use Play-Doh as it does not stick to surfaces like clay. Once the interference points are found you can massage (not beat) in clearance with a ball peen hammer and if patience is used there will be a smooth contour and not a lumpy patch of tin. For most lowering the trans mount is easiest and as long as you maintain a crank center line to pinion angle of under 4* vibration won't be a problem.

Evan