First, thanks to all for the responses! I've learned a TON going through this process, and I hope that my findings will help others who are thinking of this swap.
Current state: the car is at the exhaust shop getting the H Pipe redone. As I mentioned, the pipes won't clear the parking brake appendage located on the transmission cross member. Also, I did reinstall the original drive shaft just so the exhaust shop could ensure clearance while redoing the exhaust; however, I have a new custom built drive shaft coming (this was all part of the MDL order I placed - you take several measurements once the transmission is installed and the car is on all fours and a shop makes the drive shaft and ships it the same day).
The shifter hole - funny / interesting story. Originally, I was told by several people that I should use my original bell housing and have it drilled to attached the adapter plate (so as to move the shifter on the transmission aft to the stock position). However, I already had a late model Fox Body bell housing, so I opted to use that instead; which, as I mentioned previously, required the use of a Fox Body starter. Upon installation of the transmission, I noticed that the shifter (the rubber boot located around and below the shift lever on the top of the transmission - not the one inside the car) was making contact with the bottom front of the shifter hole by only 1/4 inch. My immediate thought: why didn't I listen to the advise of others!!!!
However, I called MDL and asked about removing my current late model bell housing and going with my original housing with the adapter plate, so as to move the transmission back the required distance...and that's when it hit me (mainly, because Bret at MDL explained it
): using a different setup (the original bell housing) would still place the shifter in the exact same position. As Bret at MDL described, all of their parts are geared (pun intended) to put the shifter in the stock position. And, it's not uncommon for the shifter to be a bit forward in the shift hole, as these cars were mass produced and not CNC machined, etc. So, the shift hole can be off from car to car. Also, it dawned on me that I would not be able to line up the transmission cross member, if I pushed the transmission back with a deeper bell housing (which would have to be a custom unit, not the stock bell housing) / adapter setup, as this would move the cross member back as well, placing cross member alignment too far aft.
In the end, I was told to either trim the shifter hole to relieve the shifter contact (which I don't want to do, as the floors are original) or keep an eye on the rubber boot that is making contact with the forward part of the shift hole. And, the cross member fits like a glove, so no worries about unwanted pressure from the top of the shifter boot touching the bottom of the front shifter hole.
I hope this all makes sense. Please let me know if you have different thoughts or perspectives.
I can't wait to drive it, again, hopefully soon!