Just took the trans out. The clutch plate, cover, flywheel all look good. However, underneath the fingers in the clutch cover was packed with the remnants of a mouse nest that was inside the bell housing. I've read similar situations where this has caused clutch slippage. Could that also have caused the noise?
The mouse nest most likely wouldn't cause this problem.
Make sure the springs in the clutch are tight and don't rattle.
Make sure the springs and fingers on the pressure plate are not loose or broken.
Inspect the throw out bearing making sure that the bearing, fork and pivot in the bell housing are all in good condition.
Check the transmission oil to make sure there are no metal filings in the oil. This could indicate an internal transmission problem and the transmission should be taking to a qualified mechanic or transmission shop to be inspected.
The best way to diagnosis this type of problem is to take the truck to a shop and have it put on a lift if you can't locate any problem.
If you are not sure of how a part should look, take it to a shop or auto part store to have them inspect the part and even compare it to a good one.
Keep us informed on your progress.
If I take a look inside the transmission what am I looking and checking for if there is a problem inside the transmission?
Do you have any experience with transmissions?
You would be looking at any metallic particles in the gear oil first.
Look at bearings, synchronizers, shift forks and gears for wear and cracks.
If you don't have knowledge of transmissions then bring it to a transmission shop or professional mechanic. Explain to them your problem and they know what to look at.They are familiar with the workings of the transmission and can detect mechanical malfunctions that a normal person can't.
Whats the best way to remove a pilot bearing?
There is a special adapter the attaches to a slide hammer. It is designed to grab the pilot bushing inside the hole and the slide hammer pops it out.
Update with my problem: After replacing the clutch the noise is still there. I've narrowed the noise down into the front end somewhere. The hub on my drivers side will sometimes turn to lock while I'm driving so I am considering replacing the hubs. Could this cause the noise?
Taking apart the front hub for inspection would be the first step before you go out and buy a new one. If the inspection confirms a malfunction then replace it.
Check the drive shaft joints on both hubs; the universal joint could be causing the noise. They could be stiff or be missing pin bearings and not able to move in all directions and could cause a clunk.
Why don't you take the truck in to have someone help you with the diagnosis, you have replaced a lot of parts and put a lot of labor into the truck. Getting a second opinion would be a good idea to confirm your diagnosis before you buy more parts.