[freeclimber]

The bearings go bad because they suck. I'm not an engineer, but I'd guess that the design or materials aren't up to the task intended.
What happens is that the needle bearings fatigue, the grease dries out, the metal starts pitting and transfering material. Soon, the crankshaft is imparting torque directly to the end of the input shaft via the binding pilot bearing, instead of the torque transfering via the clutch disc.
I've pulled the trans out of a few trucks and saw little more than dust and bits of metal left where the bearing used to be. Unfortunately, the failing bearing can cause damage to the input shaft of the trans. Bits of metal will be welded to the surface and there will be pitting too. A new input shaft is EXPENSIVE and a lot of work. If there is damage, try to clean it up gently with a file and sandpaper. Otherwise, your new pilot bearing will die prematurely.
By "clutch cylinder" I assume you mean the clutch master cylinder, which connects via pushrod to the clutch pedal. I'm inclined to say your problem is the bearing because the shifting gets worse after the truck is driven for a while.
Have you heard any high pitched grinding, screeching, scraping noises?