If it were me, I'd replace that clutch and throw-out bearing now, and wouldn't worry about losing out one some of its remaining life. There's really no way to know how much life it has left.

As for cleaning it out.... I'm shooting from the hip here, but I'd be wary of using a lot of brake cleaner. You could dry bearings out completely, and when you replace the trans oil, it might not get into all of the bearings right away, and you might wind up with a dry start for some of them. If you were doing a complete tear down, you'd put it together with some kind of lube to avoid that dry start problem, right?

I'm thinking maybe some kerosene in a good spray bottle that can put out a solid stream, and go lightly with brake cleaner on stubborn spots.

But what do I know? I've never torn down a transmission before, so I might be way off track.

 

Those aren't cracks. It's just harmless casting flash. Nothing to worry about, as every transmission looks like that on the inside.

The plastic piece fits in the back of the case and it diverts oil to the 5th gear synchro. It's called the oil receiver pipe.

You don't need to worry about cleaning it all out. Just get the sediment at the bottom and wipe the sealing surfaces with some brake cleaner on a rag. Of course, so that after you have scraped the old rtv off with a razor.

As far as other maintenance goes, you can get as crazy as you want. If the clutch felt fine, use your judgement and put it back together. If you take it apart, you'll want to torque every bolt to spec. Pressure plate bolts are pretty finicky. Also, the rear main seal is 2 piece, and doesn't require the transmission off to replace. My thoughts? It looks nice and dry in your bell housing; a rare sight indeed. I wouldn't change any seals based on seeing that alone.

 

Seeing that picture of the plastic piece the first thing that flashed in my head was that kinda looks like part of a check valve.
Best I can tell the transfer case has one for the breather. Kind of looks like this:

https://www.autozone.com/emission-co...E&gclsrc=aw.ds

Best I can tell an automatic has the "top hat" breather like the front diff.
Do sticks also have a breather?
The breathers for an automatic and the TC are located in the upper part of the tunnel.
Can be accessed from the engine compartment. Gotta grope around in there to find them. LOL.
Now how that would end up dropping into the tranny is anybody's guess.

 

The breather on a manual is built into the shift tower (or as they call it in the FSM, the shift lever retainer)

Here's pics from the parts manual that show the oil receiver pipe. It's part #32. Also included, pics of the shift lever retainer and transmission vent.