Well there you go. Going to be hard to compare that set up to any others out there. The intake clearance definitely come up, I’ve seen a more modern Jeep wiper motor used for some but your engine appears further back than some of the others I’ve seen, I don’t think the jeep one would clear the way you’ve got the bottom of that mount cut.
I don’t see how you can get that transmission in there without doing a new tunnel. I have a T56 in mine and even that required a new crossmember and a significant amount of tunnel work.
I’m assuming you’re using a factory ECU for that transmission?