The 4-synchro gearbox is slightly longer than the 3-synchro, so you need to elongate the holes in the rear crossmember (where the rear mount bolts to it). ISTR it's about 3/8". It's possible to force things together without elongating the holes, but it drastically shortens motor mount life (BTDT).
If it is a pre-TS50K TR3/A, you'll also need to massage the transmission tunnel a bit, to clear the starter bulge. Plus of course use the later starter (assuming it has the TR4 flywheel in it).
The later TR4's crankcase ventilation system was problematic, so I would probably put the TR3 road draft tube on (if the new motor doesn't have one). (Actually, my long-range plan is to re-engineer a proper PCV system, but I haven't gotten there yet.)