It is a strange problem. The fan clutch does make it look like the motor is sitting a little low. This would definitely raise the tail shaft a bit. Sometimes odd things happen when you use new parts. I did a restoration on a car, there were no prior clearance issues. (I put it together the first time too) I put the same parts back in after the restoration, and there was a major header to suspension clearance problem. There was no reasonable explanation, I just had to find a workaround.

 

Is the cross member in Backwards? not upside down, but backwards? did you use the same mounting holes on the frame as before? and the tranny mount will only fit one way correct? not possible to be upside down?

but if the mount was backwards that would push the tranny up, just thinking out loud..

 

I don't know if you can put it in backwards?

 

if the frame is like mine there are several holes drilled for different tranny's, if you used some of these holes, it MAY be possible and it MAY be the cause, just thinking???? The mounts are good, they seem to be the same number as anchor mounts? did he put new u-joints in? could he have switched those ends? unlikely? but... it is kinda crazy to see the shaft hitting the floor

 

IM restoring a 71' Cutlass S with a 455\TH400 swap from a 350\TH350 original car. When I got the car, after working on it a while, I dropped exhaust and drive shaft and noticed similar thing was going on when P.O. had the car. Looks like he modified floorboards a bit to stop it.
so far Ive replaced all body mounts, engine mounts (if its a 350 car, use new 350 mounts and original 350 frame mounts), and trans mounts with an Energy Poly trans mount... it is once again too close to the floorboards! As someone mentioned ealrier, there is a spacer on the new poly mount. Even if you remove the spacer, the New mount is still much taller than the cheaper stock one.

When I get to that point in restore again, I might just put stock one back in to lower it away from floorpan a little bit more and see how that goes. I also wondered about it being sagging floorpan. Im going to swap portion of mine out (in this area of tailshaft) later this year so we will find out.

Taller enigne mounts will push engine up into the valley under firewall area more. It will tilt engine up in engine bay a little, but angle axis of engine\tran little lower at the tailshaft. But cause of X-member being fixed, it shouldnt matter at that point as x-member doesnt move. Crossmember being the same, changing the engine mount shouldnt matter much at the tailshaft spot.
One thing I did notice in my restore is the open frame rail is slightly bent upward on one side near x-member mount area, where someone obviously put jack to lift car instead of the correct spot to jack it up. This could come into play a little bit too. Could be several little things adding up to the problem.

Replacing engine mounts will also help centering issues of the fan in the shroud, which I had. Especially since engine mounts dont sag the same rate on both sides, as mine were. Engine was slightly tilting, causing centering issues with the shroud.

It is kind of crazy that you\I put all new mounts in everywhere, and you get this problem as a reward!