Well I got a chance to look at things tonight and their is for sure some issues, aslo with the rear end I am guessing. Here are some pictures and dimensions that I got. Maybe you can give your opinion on where to go from here.

DAYCLONA based on your measurements you have aprox 6-1/2" from the cross member bolt to the top of the tunnel. I only have about 5-3/8", something is funky between the two of us on that.

Also I don't know if it suppose to be but the tranny is offset to the drives side about 1/4" based on measuring between the cross member bolts.