When you replaced the clutch, did you replace or service the pilot bearing?
My truck sat for several years after I got it, before finally getting back on the road again. After that extended down time, it would grind while shifting into any gear from neutral when stopped. It was also a little trickier at times to shift into some gears when moving (trans is unsynchronized in all gears and yes, I was double clutching).
Cutch freeplay was fine. I could feel a fair amount of movement- so it was not like I wasn't getting enough travel.
The trans always had a noisy 5th gear, so when I pulled it to check into this issue, I also removed the clutch for inspection. The clutch driven disc and pressure plate were great, however the transmission input shaft had wear marks where it contacted the pilot bearing. I checked the bearing (ball) and the grease in it had turned into something extremely stiff and very un-grease like, making it almost impossible to turn the bearing. I think this caused the input shaft to turn inside the inner bearing race, which caused the wear and kept it spinning enough when the clutch was disengaged to cause problems.
Installed a new bearing, and no more issue.
Best Regards...
