Ross,
You are having a bad day to say the least. First as a test I would remove the torque converter and see if you can get the halves to line up easily and bolt down. If they do not, see what is causing the interferance. If it is the flywheel remove it and again see if you can bolt the two halves together. If you can at this point, double check the part numbers on the flywheel you have. If your torque converter is causing the problem, if you have the old one there is a code on the back of it in the center a or b. Do you have the same on the replacemnt? There is a guide pin on one side of the engine that aligns with the corresponding hole in the atx. This may be binding. Get a round file and file out the hole a bit for the guide pin and see if it slides in place then. Mine was binding here and I filed it out a bit and the tranny just slipped. in place.
As for the top mount bolt, I don't have one to look at right now, but if the atx is still sealed at the point that it broke off, I'd use jb weld great stuff. When I rebuilt my tranny the inside of the case was cracked and I used this and all is fine.
Take your time...
Bob
