Have been through a rebuilt FJ box before and I wouldnt bother again myself, the syncros crapped themself pretty quickly afterwards with some spirited driving as the are fairly weak. One miss shift in the heat of the moment and they would be dead again.
As for gearbox options, I'm currently running an RB20DET twin syncro box, not the strongest box out (around the same strength as an FJ box though) but the syncros are smooth as, they are cheap (around $500) and I personally have seen them handle 200-220RWKW FJ20's fairly well with no dramas and they have very similar gear ratios as standard. Other then that there is the RB25 box if you are worried about popping boxes, you will never break a 25 box however these are expensive ($1500+)
Both need the same mods to fit which are fairly simple. Just need 2 top holes of the bell housing elongated, and your gearbox cross member will need to be modified as it sits about 1" further back, I have done 3 of these now for me and friends. Gearstick comes out in the standard position and tail shaft is the same for RB20 only need a new tail shaft for RB25/Z32 as they are longer and have a different output shaft
Then as others have said the Z32 option, I haven't mucked around with these before so dont know much about them except there are about 10 different variaties and gear ratios out there, and your looking about the same strength as an RB25 box.