I have a 99 Ranger with a manual transmission

So yesterday and today I got caught in about 8 hrs of stop and go traffic in 90+ heat. Before I even left I noticed the clutch was extremely bumpy when I engaged it in first (like it would engaging late) and when I switched from 1st to 2nd gear. By for about the last hour or so the clutch started to make like a light grinding noise when I was at a stop with the clutch pedal depressed. If I put it in neutral and remove my foot from the clutch pedal the sound would go away. Cut to a few hours after I've gotten home, the clutch makes a grinding sound when I switch gears and the RPMs will pop up suddenly and immediately correct themselves when I am driving (you wouldn't noticed if you weren't watching the dash its so quick).

Little bit of background info:

The clutch was replaced about 2.5 years ago

About 3 weeks ago I was having trouble shifting into gear and noticed my Clutch Fluid Resevoir had gone empty. I refilled it and the problem went away but I never bled the lines.

My truck has been bumpy when I start for a while now ever since I struggled to get out of a tight spot on a hill and burnt the clutch (maybe a year ago) and I've always attributed that to possible hotspots on the flywheel.

Any suggestions or ideas as to what I could do or look at?

 

Well the throwout bearing sounds like it is on the way out, it is part of the slave cylinder.

When you push the clutch pedal in the slave cylinder expands and the throwout bearing is pushed against the flexplate(which is spinning at engine RPMs), this relaxes the grip of the flexplate that sandwiches the clutch plate against the flywheel, so clutch plate(attached to transmission input shaft) can now spin at a different RPM than the engine, so you can shift gears or stop.

If there is a noise when clutch pedal is pushed in it is almost always the throwout bearing, could be pilot bearing but doesn't really matter since you change that when ever you change the clutch.

You also have a leak since the reservoir ran dry.

Master cylinders don't usually wear out, but that wouldn't be part of a noise issue in any case, they are not to expensive, under $50 usually.

You do want a self-adjusting Flexplate if you decide to replace clutch system.
And never get a "racing clutch disc", they are made of softer material to get "sticky" when warned up, which is great for racing but truly sucks when you have to replace it every year.