Problems pilling up!! Need help!

[Alloutaggie07]

My problem started when one morning on start up the car started to shake. It was so bad the exhaust would rattle and after a few minutes it would stop and not come back until the car sat for a while. After a few days of this I started to notice a grinding/whining noise coming from the rear end. It seemed to get louder as I increased speed but would fade or almost go away when I let of the gas. I took it easy and on my day off went to the parts store. On the way I notice each time the car shifted from second to third a loud clunk would now happen in the rear end. At this point I started with the simplest things. I replace rotors, pads, bled all brake lines with new fluid, changed fluid and filter in trans, new coil packs, wires, plugs. After all this I still have the shake at start up, still have the grinding/wing noise but it is louder, still have the clunk noise, and now it seems as if it bogged down. I have read t ton of post on bearings, u-joints, and the nut in the differential backing out. At this point I will take any advice yall have. Tell me what to check and what to look for and ill post the results. I am a broke college student and need to get this car to last a few more years till graduation so any help is appreciated.
My car is a 98 3.8L auto with 130k on it. If you need the rpo/option codes for it I will list them.