i don't think anything is perfectly centered or square on these cars... looks like you are within 1/2" overall, which is probably about as good as it gets...

 

The issue is that the tail shaft is so far over to the passenger side that I cannot put a bolt through the crossmember into the trans mount.

 

I'm not the most experienced person in the world with this stuff, but I have the same issue evertime I put a muncie 4sp in one of these cars. My sollution everythime is simply pushing hard on the tailshaft of the trans in the direction I need it to go until I get the bolts worked in. I've never had a problem as a result of doing this.

 

The stock motor mounts/frame stands have somee adjustibility...if you tightened the motor mounts down first or are using aftetmarket frame mounts..
There lies your problem...

 

I had the same sort of issue. In my case, it was 100% related to engine mounts on the frame. The mounts should have a bit of play them, and my approach was to loosen the bolts which connect the mounts to the frame, then try to center the transmission and see how much force it takes. If it takes a reasonable amount of force, and stays in position when centered, then put your trans bolts in, and re-tighten the mounts. You might then want to remove the trans bolts to check if they came under stress when the mounts were tightened. You might end up having to elongate some of the bolt holes to get things to line up. Let us know how you end up fixing it.

 

^^^^This....

I had to do this when I first built my GTO, which had a BBC. I bought repop frame stands and they did not position the engine properly. In my case, the tailshaft was shifted over to the drivers side. I elongated the frame stands a little and centered the transmission. And wouldn't you know it, after doing that, my headers fit perfectly.

Andrew