changing the pinion seal isn't too bad, but I guarantee your clunking in the rear is a worn out limited slip since you have one, this is the spider gears I pulled out of my '00 Explorer that I picked up hoping that this was the only problem with 206k miles:
As the clutches wear out the side gears move further and further out causing a decreased contact patch on the spider gears, when they get bad enough the above happens... but before that they clunk from the added backlash...
Rebuilding a limited slip isn't too bad, hardest part is getting the S spring out and back in... and hopefully the cross pin bolt isn't broken...
For the record I pulled the axle apart (you only have to pull one axle shaft to get the spider gears apart and rebuild the L/S), hosed it out with brake clean, threw in some junkyard spider gears and clutches (rearranged so it goes clutch to steel instead of stacked steels... and added one on each side) and have put over 50k miles on it towing and such, only something in the front makes noise...