Been researching this for a year or so myself. I originally settled on the Audi 5HP19 5 speed automatic (02 model) because it uses a stand alone computer for the gearbox. Several Audi websites revealed multiple trans guys to build one as mild or as wild as you want, but the base box will take 300ft lb torque. I attached it with a 1" aluminum spacer plate to a 32valve 5.4 Navigator engine with an adapter sleeve/spacer to mount the Audi flexplate to the crankshaft. I kept the Lincoln flexplate to use with the starter.
My project is not a GT40 and the 5.4 engine is so short, I need the engine moved farther forward than this combination allows, so I'm either going to have to make a longer crankshaft spacer and a longer engine adapter (almost a bellhousing), or try something different. Tentatively, I'm now using the 4R70W automatic that came with the Navigator, with a 1/2" aluminum adapter plate and a splined adapter shaft to mate it to a Corvette Getrag differential. The Ford tranny is shorter than the Corvette tranny, and besides, I have it!
That doesn't matter to you guys, the 5HP19 would be best. It has the same bolt pattern as the Audi manual transmissions, so you could probably use a Kennedy type engine adapter, but still might need the crank spacer to fit the Audi flexplate. Mine basically just looks like a short thread spool (bobbin?) with the Ford crank holes drilled in one flange and the Audi holes drilled in the other flange. Don't have a picture of the flange, but I do have a trans pic from the Ebay auction. Also a shifter pic from an 00 01 Audi A4.