its lacking sufficient light.. its stretching.. and the only time mine lost leaves.. was due to over watering ... i would root a few pieces... just in case.. thats some scaffolding you got going there.. ken

It's doing whaat? That doesn't sound normal. Please post a pic. Whaat?...it's been dead around here lately n_n Just kidding. (hangs head) It's perfectly normal. =D

The rot most often starts at the bottom and move up. I believe that the tissue does not brown with age. Take plant out of the pot and inspect the roots. If rotten or dry, cut them off. Healthy trunk will grow new roots. Trunk should be checked for rot; tissue should be light colored without any brown/dark spots or rings. If you suspect rot in branches, check them all by slicing ( - clean the knife/scalpel/blade with alcohol between cuts - ) as you already did until you find healthy tissue. I think that rooting hormone contains some fungicide, but you can dust with cinnamon (I used it on large cuts). I am not convinced that rooting hormone will help growing new roots... Grafting will likely not work...someone here tried but I am not sure if it was real success. See a post by very good grower hanzrobo - click here (there are more posts on same subject). Healthy trunk will grow new leaves and branches. I would not remove any healthy leaves, they actually help plant grow.

I agree with Mike above, and other posters. It is kind of late to repot, but you already bare-rooted so just finish it best possible way and let plant to recuperate (jades are quite sturdy plants and it really shouldn't 'suffer'). It would help if you indicate your general location or at least a growing zone. I would divide it (at least that one smaller trunk...), but leave that for next year or year after. If you can get some grit and add that to potting mix, it would be better draining IMO. Keep soil to max 30%, and balance equally split between perlite & grit. Plant has lots of etiolated growth, so you should figure out better lighting - maybe some supplemental lights. I would shorten up/prune some of the etiolated growth, and you can use prunings to start new plants. Since you sprayed off the soil - may I ask why not all of it?