Hello And Looking For Manual Transmission Options For 2001 Mustang Gt

Hi,
First post here.

I just bought a 2001 GT, convertible, factory 5 speed. It's a one family car since new, has 54000 original miles (confirmed by carfax). I'll pick it up in a week.

The story is that it was being built by a Ford tech. Unfortunately he passed away before it was finished. That was about 3 years ago. I bought it from his mother. The car has sat since in a garage. It's been outside for about a year. After the guy's death, the transmission and the supercharger that were to go into it were stolen.

The engine has been rebuilt with the thought of putting in a supercharger, built strong, I'm told. The engine is in the car as a long block, nothing else. I will not be adding a supercharger, but will go with a factory intake setup. The engine still turns over by hand. I will pull the engine and go through it before first start.

Right now, I'm looking into finding manual transmissions to put into it. Cost is important!
I have found a 2008 TR 3650 with 26,000 miles on it for $500. Can I make this work with a 2001 4.6L. I understand I'll need to shorten the driveshaft by 2". What else?
Thanks.

From what I've managed to gather is that the tranny will bolt in and should work. The issues will be that the newer 3650 is actually shorter, so I'll need a longer driveshaft. Maybe the driveshaft from a '05 and later will also bolt right in and everything should be good.
I won't be trying it. I'm going to go with a junkyard 3650 from a 2003 GT and rebuild it myself,
This will be my first tranny rebuild and I'm looking forward to it. From what I can tell, it shouldn't be too difficult.
Thanks.