hey Jon ,,, when we put the B15 in my egg there was a few alignment problems as well (tilt problems)and the way I was able to get it lined up correctly was I jacked up the rear of the motor because it was a little bit tilted, you can see it close up as you raise the rear(only) of the motor only had to go { } this much ., LMAO, you may have to pry the mount a little bit as you start the bolts but it should line right up... I never touched my cross member...
and whatever you do Don't give up on the bolts,, MAKE sure you get them All in ,, they suck trying to get lined up but after you get 2 its a breeze
it was hard to see all this underneath the car,, lol .. glad I had a second pair of eyes to see what was going on,, oh and the extra hands to help turn wrenches was good
and as long as you have the TOB in correctly it should work,, mine seemed to get stuck when moving it by hand..... just greased up the shaft (lol) and it works great,,
also if you may have to modify the shift rod area for shift clearance,, I had to, got pics...
hope this helps