rustygreenf150

so, while going say 60mph with nothing seemingly wrong, I put in my clutch at which point my truck begins to make a nasty grinding sound with a bit of vibration. As I finish putting it in neutral and release the clutch again, said sound gets louder and vibration gets worse. I was luckily near a station and stopped to look but nothing seemed wrong that I could see. I turned around to head home about 25 miles. It runs as if nothing is wrong while in gear but in neutral or with the clutch in it sounds like I opened pandora's box.
I stopped at a parts store in a few miles thinking I'd check the trans fluid, which was about 2 quarts low. There was some leakage around the rear main seal?? of my transmission and I'm thinking that leaked out and I burned something up inside my transmission.
Any thoughts on this issue. I don't want to replace the transmission and find out it's something else. The clutch probably has like 8k miles on it maybe 10.
Thanks for any insight.
FYI 1994 4.9l 5spd ext cab 2wd 196k

dirtcrew51m

Jack the rear off the ground, put truck in neutral, go underneath and turn the driveshaft, listen or feel if anything is grinding or does not feel right.