Robert
I echo the comments of Mark and Alan. If I recall correctly, the GT engine is very wide, much wider than a "standard" V8. As far as using the transaxle, I think this has been discussed several times on this forum in the transaxle section.
As Mark said, you can easily build a "standard" V8 with a lot more power for a lot less money, maybe less than half of what you'd spend for a Ford GT engine (and that does not even consider the higher associated maintanence costs). And as Alan said, 600+ HP in a GT40 is not that uncommon.
On the surface, it would seem to make sense that a Ford GT engine/transaxle combination would be ideal for a GT40. But, it seems better suited for the Ford GT than it does a GT40.
If you're seriously considering this combination, the very first step is to contact the GT40 manufacturers and ask them if it will fit in their cars. If they say no, then the decision is pretty easy.
Eric