Two options.
1. I like rbohm's for simplicity (The C3/ALD4, and later automatics have detachable bellhousings which can be converted from the donar engine to fit any other of the later 4 or 5 speed gearboxes. They have been adapted to manual gearboxes too. In NZ, our 2.8 and 2.9's could be mated to a Toyota 5-speed with steel adaptor and a special intenal hydo clutch. There is a common internal throwout bearing hydraulic clutch used by racers, and smaller SFI rated clutches/flywheels which fit the 6 bolt Cologne and Vulcan cranks without much fuss that can be joined to the old automatic flexplate so the stock starter can be used. Sounds complicated, but you then get a good manual gearbox and stock starter)
2. The rear driving via a rear mounted transaxle is an invloved problem if your using a Taurus body. The Fiero, MR2 and Ferrari Mondail 8 used an engine used in a front drive car (X-car, fwd Corolla, fwd Lancia Thema V8).
As soon as you use a 2-door or 4-door sedan and mount the front engine in the back, you have to find a method of venting the engine, and strenghtening the rear bulkhead to use the front power pack. You have few space issues, but its possible to run polycarbonate windows with NACA ducts and use the back light(rear window) as a low pressure extraction zone. The area behind the b pillar has to be double glazed, and the whole rear from there to the C-pillar treated like a pick-up truck. If you can do the metal work, your in.
The front drive transpack is forward mounted with the trans below and behind the V6 engine. It gives perfect 50/50 balance.
Issues are that the steering arms have to be replaced to become a strong radius arms to lock the front wheels on the strut IFS. The geometry (camber, castor and spring rates) needs to be reset. The effective droop in the rear suspension needs to be different to the front, and the angle of the struts has to be the same as in the front. The designed in anti-dive for rear suspension has to change, but your stuck with it.
All in all, the FWD to rear drive set-up with the transpack is a lot of work, but it would be a killer silhouette formula. Especially with a proper 95 on wards Lincoln FWD quad cam 4.6 V6 and auto gearbox, able to shift the car at respectable speed.