Hi Adrio,
There are more issues than have been mentioned.
In addition to the synchro first gear, somewhat later gearboxes also have a heavier and stronger flange on the bellhousing. By later, I think post-TR4A, but I'm not sure exactly when the heavier flange was implemented. Depending upon your use of the car, that might be a consideration. On the other hand, if originality is important, you'll likely want the thinner flanged gearbox.
More importantly, 4A and later use a different input shaft. The "nose" that fits into the pilot bearing at the rear of the crankshaft is longer on gearboxes up through TR4, than it is on TR4A and later. You can mate up the later gearbox to the earlier cars, but will find it impossible to fit the TR4 and earlier gearboxes to a TR4A or later car - that uses the smaller, diaphragm clutch - without more modifications.
In other words, if you stand the TR4A-TR6 gearbox on end, on its bellhousing, it will sit level because the input shaft is short, roughly flush with the bellhousing. The TR4 or earlier gearbox won't sit level if stood on end, because the input shaft is longer, protrudes past the bellhousing. Also, the clutch splines don't match, and I think the throwout bearing carrier (aka "front cover") is also a different diameter.
I doubt the "guts" of a TR3 gearbox could be used in a TR4 or TR4A box, anyway. The two are slightly different overall length and a lot of the internals differ, particularly around the 1st gear cluster.
You might want to find a buyer for the spare TR3 box/OD and use the funds for a TR4A box/OD, or to build up and convert the non-OD TR4 gearbox you've already got. But, even with the latter you are going to need more than just the mainshaft to get it to fit up to a TR4A.
Alternatively, one of the vendors might work an exchange with you. Some only offer A-types and OD gearboxes in exchange for like-units, but would probably be happy to get hold of an early TR3 gearbox/OD, if you really want to let it go.
I was going to recommend Quantum Mechanics, too. I'll be sending them my A-type OD for a rebuild. I think The Roadster Factory does some gearbox/OD work, too (or farms it out to someone). Quantum's name is the one I hear mentioned most often when it comes to OD units.
Quantum does sell the special main shaft, the adapter plate, inhibitor switches, etc. to convert a TR4 non-OD gearbox to OD. You could then use the A-type you've already got.
If you end up building up a gearbox, it's a good opportunity to upgrade a few things. For example, the input shaft seems to benefit from extra roller bearings. A-type ODs can be upgraded, too.
If you exchange a gearbox and/or OD unit, be sure you know what you are getting. The A-type has early and late versions. The later one is a little softer kicking in, due to a smaller accumulator piston. There are a lot of non-TR A-types around, although I don't think most knowledgeable vendors will try to sell you one, since the rear mount would probably not match up.
It's a different matter with gearboxes, though. There are many sedan and other gearboxes around being rebuilt to TR specification. That might be fine, functionally, but might have a few details that are unoriginal.
If having one rebuilt, have both rebuilt. Since they share oil, there is too much likelihood of cross-contanimation if one or the other is old, while the other is freshly rebuilt.
Let us know what you end up doing!
Cheers!
Alan Myers
San Jose, Calif.
'62 TR4 CT17602L