Why do you want to get a 3650 for your car.
From wourking with Modular motors and 5.0 motors. The bell housing mount different ways.
THE 3650 bell housing mounts from the inside with 10 or 12 bolts. A standered T-5, Tremec 3550 The bell mounts to the trans from the outside with 4 bolts.
I don't think a 5,0 bell will mount to 4.6 motor and same for 4.6 to a 5.0. So you would probally have to get a bellhousing custom made.
You are probally better off finding a nice Tremec 3550 and throwing it in. I had one and loved it. I wish I never sold the thing. If you need stronger I would go with a Tremec 500 or 600 then.
I just looked at one company that makes a 4.6 bellhousing that
Fits, 3550, TKO, TKO 500, TKO600. But they don't offer a 5.0 bell that will fit a 3650.
I would call them and see what they say. They can help you more.
http://www.ddperformance.com/index.php