[dsraven]

it's a dillema for sure, where to place the angle finder. the trans shaft has some play in it because the yoke isn't in there to center it, the amount the bolts on the engine oil pan stick out depends on how thick the aluminum casting is under the bolt and the casting thickness can vary because that bolt head surface isn't machined, etc etc. you could put the angle finder on the vibe damper of the engine I guess.
to answer your question, the trans mount pad needs to be parallel to the trans mount surface. also, it may be a good idea to assemble the whole thing and have a jack under the cross member to hold the weight of the trans against the rubber mount, otherwise the angle gets skewed when the weight of the trans crushes the rubber some. personally I always leave a bit of room there so I can shim to get the angle right. \I fab a shim from flat stock and use that under the mount, between the mount and the cross member. if you put it dead on then there is not room to work with if you have a vibration, or whatever, down the road. can you use vice grips or ratchet straps to hold things on each side frame mount while you mock up?
if you have a yoke for the trans you could slide it in and put the angle finder on that possibly, depending on how nice a fit the yoke is with the trans bushing. you would need to take the rest of the driveshaft apart to get that unless you have a spare one that will fit. maybe the driveline shop would loan one knowing that is what is keeping you from having them work on a driveshaft for you. just some thoughts.