Well I emailed Mac and got a very quick reply for all these questions.
1. The shifter does not sit in the stock location. It is about 4 inches farther back.
2. I will fit the trans tunnel. All tunnels are different so a BFH might be needed to persuade it.
3. A new drive shaft is needed.
As far as the noise from the engine, I believe it to be a loose flywheel. At least that is what I hope it is. When doing the swap 10 years ago, I remember not using locktite and forgetting to put in the dowel pins. I also installed one of those "amazing" cheap xtd ebay clutches and flywheel. I know this is not acceptable but I was a kid and not very patient with my work. Times are different now. We did a compression test and all cylinders were 160 or above. That is fantastic! My oil looks good but I should send it out to get analyzed. When I get it back I will drop the tranny and replace the clutch/flywheel and torque everything to spec with locktite. Hopefully this will work. If not, 10k later and I will have a built motor.