Bob,
Short answer: yes
Longer answer: the original ZF gearbox had an input shaft of a certain length, as did the first evolution which was called the /1 version. When Ford and De Tomaso got together to produce the Pantera, the /2 version was created which superficially looks the same, but is improved and changed in numerous ways. The case is physically bigger, almost all internal parts are different, and (here is the answer to your question) the input shaft was longer.
The early Panteras used /1 gearboxes left over from the Mangusta program. They were partially dismantled and the ring and pinion were flipped, as the Pantera was designed to run the gearbox in an inverted orientation. The bellhousing was deeper, long enough that the input shaft was some distance from the back of the crankshaft, so an adapter was fitted that slipped over the snout of the input shaft and indexed inside the pilot bearing in the crankshaft.
The /2 version used a different bellhousing with the same depth as the /1 bellhousing, but larger in diameter and with a different bolt pattern. The /2 input shaft is longer and reaches the back of the crankshaft without need for an adapter.
If you have an original-style GT40 bellhousing, it will only fit an original or /1 gearbox. I think Safir makes a hybrid bellhousing with a larger diameter and different bolt pattern to bolt to a /2 gearbox, but if it's not also thicker, you would either have to shorten the input shaft or run a spacer between the bellhousing and block.
Or so it seems to me. I would speak to the Safir boys and Paul Fleming and see what they have to say....
BTW the BMW M1 gearbox input shaft is a LOT longer than a Ford /2 which is why it's not really practical to buy an M1 box for GT40 use...