I have a 99 4x4 5 spd. Put a new clutch in, new slave new master cylinders. Ran great for a while. Started to give me trouble going into 2 nd gear. It was intermittent. And when it happened it would get worse on longer drives, next morning.. Nothing, no problems. Then it started to grind when I let the clutch out, then when it engages, grinding goes away. It's like the clutch isn't engaging, once it gets moving, and I'm up to speed, it shifts fine. Until I stop, then it does it again. The only thing that has happened since I put new clutch in, is I loaned it to my cousin and he hooked up a trailer to move. May have loaded too much weight, but he says no. Other than that it ran and shifted great for the first 3-4 months until it started to give me problems going into gear. Then the grinding started a few weeks later.

 

Welcome to the forum

Doesn't read like any common issue

When the clutch pedal is down the throwout bearing and Pilot Bearing are both being used, either could make a "grinding" sound

The way this works is that the transmission and gears are connected to the rear wheels there is no disconnect for that end
The clutch disconnects the transmission from the engine

So when you are stopped the transmission and gears are at 0 RPMs, have to be since they are all connected all the time to rear wheels
If running at idle the engine is at 700 RPMs
Neutral allows part of the transmission to spin at engine RPMs and the other part to spin at rear wheel RPMs

If stopped when you push clutch pedal down it disconnects transmissions INPUT shaft from the Engines flywheel
This allows the INPUT shaft to slow down to 0 RPMs so transmission can be put "into a gear" that is also at 0 RPM
If pushing gear shift into any gear causes grinding then INPUT shaft is NOT at 0 RPMs

Each gear has its own synchromesh "gear", its a softer metal used to "match spin" when changing or engaging a gear, grinding when pushing on shifter means the INPUT shaft was NOT at 0 RPMs and is having to be slowed down to 0 RPMs to "match spin"
Or grinding when changing gears while moving, INPUT shaft and gear have to be "matched" to the same RPM or no engagement is possible

Air in a Hydraulic clutch system is a common issue for grinding, because clutch is not FULLY disengaging INPUT shaft from flywheel, so INPUT shaft can't slow down(or speed up) to "match spin"


INPUT shaft has a bearing inside transmission, and it has a Pilot bearing inside the crankshaft/flywheel to support that end of the shaft
The Pilot bearing allows the input shaft to spin at a different RPM than the crankshaft/flywheel, so slow down or speed up, so its only used when clutch pedal is down, the rest of the time the INPUT shaft and crank shaft/flywheel are spinning at the same RPM

Throwout bearing allows the fixed Slave cylinder to release the spinning pressure plate, it is also only used when clutch pedal is down and slave is extended

Either of these would make a noise any time clutch pedal was down, not just when moving the shifter into a gear