Yep, those go behind the spider gears, I found the same thing on a 6mt I bought to swap in. Bummer..
On the subject of clunking when warmed up, my problem is persisting after replacing the center differential, it seems like it might be the rear differential so I'm replacing it next week.
After the c diff replacement I jacked up a single rear wheel after a long drive and turned the wheel while in neutral. The result was a very difficult to turn wheel that would pop and release l like the diff was binding, once it cooled off it was easy to turn again.
Also when the warmed up while driving, locking up the brakes on the snow (abs fuse yanked) there is an awful grinding noise. I'm hoping this is also the rear diff as one wheel stops rotating first.
I'll let you all know how it turns out, getting tired of fixing this old clunker!