Jeb:
I concur with the clutch and gauge suggestions. Replace both, soon.
A decent clutch assembly runs about $200. (the Ford 'Valeo' unit, for example).
A new, stock, flywheel (iron) runs $100.
I recommend replacing the flywheel but if it's not cracked, it can be resurfaced for $30. or so. Check around. Labor charge varies a lot; I would guess at least $100., probably more. Again, get estimates.
Replace the rear seal, as previously recommended and hope you just need new U-joint bolts for the other noise.
A new clutch may cure the shifting problems but have the transmission oil changed while it's out. Try to get synthetic if you can.
Let us know how it all works out for you.
BTW: Love your User Name.
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