Great news about the exhaust. Bet it sounds great.
Now you know the dilemma I had when I tried to pull my 4 speed out the bottom. In addition to pulling the engine/trans as a unit, I had to remove the floor hump to get the trans up high enough to pull off the trans crossmember…what a nightmare! My BCW crossmember was welded in place. I cut it out and made it a bolt-in.
Your CMC uses the OEM Pinto crossmember if I recall building the Ford based CMC TD I had. I guess you can’t get at the bell housing bolts from up top then lower the back of the trans to get the lower bolts? You can get at the flex plate bolts through the starter hole (after removing the starter).