Yeeh our SJ had similar issues after wading through the water. I fully relined the rear brakes, cleane dup all of the handbrake linkages etc etc and we have been sort of fine since.
We did also find that the type of mud seemed to have an effect on how it behaved after. Sticky crappy stuff seemed to stay in the drum and not allow the rear foot or hand brake ot work very well after. It needed removing and cleaning before it worked properly again
I do think that the water in there doesnt do it any good and we did find some rust developing inside the rear drums too, quick clean and adjust and off it goes :)
If you need parts, PM me and I will let you know of a local motor factor who can get most bits at alot less than main dealers