Several people have reported that the later, shorter cover works OK with the early clutch. But I didn't try it, since I installed a TR4A diaphragm clutch at the same time I put in the late TR6 gearbox. It is important not to use the longer cover with the diaphragm, as the fingers will hit the cover when the clutch is released. And of course the TOB & it's carrier need to match the clutch.
The rear crossmember needs to be modified a little, as the 4-synchro box is about 3/8" longer than the 3-synchro. I found that I had to bend the lip as well as filing out the holes.
Depending on the vintage of the gearbox, you may need longer studs for the 3 studs at the top. Also longer bolts.
The thicker flange also moves the slave cylinder a little closer to the lever; I had to shorten the pushrod on mine, but you might not need to. On the 3A, I also fabricated a mount to stretch the spring tighter (make up for the relocated slave bracket where the spring normally attaches), but I'm going to try leaving it off on the '3. If it does turn out to be needed, I can always add it later.
A new pilot bearing is probably a good idea anyway; the TR6 input shaft is a bit shorter than the TR3 shaft, but it seems to work OK.
That's all I can think of, offhand.