If the noise goes away with the clutch to the floor it sounds like it could be the input bearing on the transmission.

If the noise goes away with the clutch released and in the up position it could be the throwout bearing.

 

When the clutch is on the floor the noise is gone, which is why I don't think it's the throwout bearing so sounds like it would be the input bearing. It doesn't do it all of the time, I really tried to pay attention to it today while driving around. Couldn't really notice any particular pattern or cause

 

I think it might be your throw out bearing. If the noise goes away when you put pressure on the clutch pedal your putting actual pressure on the throw out tightening it back up. With pressure off the pedal the throw out is just spinning there, if its not a good bearing it will make noise. And honestly ive seen them make noise both ways, with pressure or without pressure....

Im betting the Clutch fork has nothing to do with your first gear shifting issues. Its your syncros inside the transmission. Ive had this issue for the last 50K and have had my transmission out twice, once to replace the clutch shift fork and nothing changed in regards to shifting gears. When your shift fork is bad you will not be able to shift gears with motor running.

The shift fork is usually fine with a stock clutch, its when people put a higher HP rated clutch in that increases the pressure needed to disengage the clutch and puts more stress on the fork causing it to snap.

If it hasn't been replaced your clutch is at least 15 years old. Bearings wear out from sitting as well as use.

If you plan to replace it buy the upgraded fork and a new Shift Fork Pivot Block. Its a $5 plastic piece known to get brittle and break. It sucks pulling your transmission to replace a $5 part. Ask me how I know.

 

Awesome information. Always learn something on here. I figured if the transmission has to come down might as well get it done while it's all there, clutch and everything else. I'll definitely keep it in mind about the upgrades

 

This could also be a "normal" sound associated with the zf6 transmission called "gear rollover"

What condition is the insulation at the shifter boot as well as the boot itself? Have you serviced the transmission with new oil? I prefer pennzoil synchromesh in all my manual gear boxes.

 

It's definitely not the normal gear rollover as it happens when I'm at a complete standstill. Once I start moving at low RPMs I'll get the rollover and it's definitely a different sound (although similar), but I am due for a service soon. Previous owner claimed to have done one recently but I need to get on my own schedule

 

It's definitely not the normal gear rollover as it happens when I'm at a complete standstill. Once I start moving at low RPMs I'll get the rollover and it's definitely a different sound (although similar), but I am due for a service soon. Previous owner claimed to have done one recently but I need to get on my own schedule

 

This is a video of what's happening. Note this is not me or my truck, and my noise is not nearly as severe as that but otherwise that's pretty much it