Hi, my truck has had growing problems for a while now. It started out with the second to third shift grinding unless I shift slow and double clutch. Then all the shifts after second started getting difficult. For a long time, it has been difficult to shift into first, but now I really have to muscle it in and a lot of the time I feel to really strong clicks. More recently, I noticed this loud grinding noise that happened toward the lower rpms with a lot of throttle, and was intensified by the cold. Now I notice a vibration through the shifter and floorboards when the rpms get high (in gear). It even makes a noise sometimes that sounds like a big rig engine braking. My mechanic says the grinding noise is the input shaft but he says not to worry about it. What do you guys think?

 

Sounds like a throw-out bearing spinning in the fork to me....whatever it is, grinding sound and feel, is not good! It needs to be fixed....
Could be front bearing snout might need greasing for smooth throwout slide, but that would not cause it to be hard to shift above 2nd gear. Unless you have some clutch drag. That could be anything from bent fingers, bend input shaft, bad throw-out, etc
Drain your trans fluid, and refill....looking for glitter in the oil or tell-tell metal shards. Syncro's and sliders might be worn....

 

Clutch Drag could be the problem. Sometimes when I'm backing up and hit the brakes with the clutch to the floor but the transmission in reverse the engine rpm will bog a second, then come back.

 

I took the shifter boots off for a day and noticed a bad sound when the clutch is released, like putting it in neutral at a stop light. It sounds like a bearing might be spinning.

 

Believe your thowout bearing is going or gone. If you were in reverse for a second when the clutch was on the floor, the trans grinding or truck moved, clutch was not disengaged.
Need to pull the trans and look. Is the grinding sound all the time while the motor is running? Or when you push in on the clutch? 99% of the time, throw out bearing, sometimes front trans bearing....either way, you'll have to scoot the trans from the motor to change it....