The pilot bearing is the bearing (used to be a brass bushing/sleeve which in reading, your's might be as well) that sits in the end of your crank, and the front shaft of the transmission sits inside it. It basically is a friction point for the two when the transmission is engaged or disengaged, or in neutral, and the bearing spins, eliminating the friction. To my knowledge, there are none that are grease-able, they are sealed and a part that can go for years and thousands of miles, or die when ever they feel like it. They are not a continuously turning bearing, so they can achieve a long life span. Other than maybe "riding" the clutch pedal, they are pretty much unaffected by anything else going on. To give a case in point, my SII has the original bearing in it, and it is 30 years old with 145K on the clock. If yours is a bushing/sleeve, it is impregnated with oil to lube, and will basically wear out and allow slop (vibration) or seize (like it sounds like your was doing) causing hard shifting as it slows the shaft too much. Sleeves can last just as long as bearings if they choose to, and don't see abuse. Constant friction causes heat, which can cause galling, which leads to seizure.
The release bearing, also known as a "throw out bearing" is what turns on the main transmission shaft when you step on the clutch to engage the clutch. It turns at engine RPM until you release the clutch (to go or putting in neutral) at which point it stops turning, unless the clutch is out of adjustment. Yours may or may not be grease-able. Most new ones are a sealed bearing as well, or use the hydraulic fluid to lubricate. Older cars used linkage for the clutch actuation, where as most everything new are hydraulic, many using brake fluid as the hydraulic fluid. Good thing about hydraulic is they are constantly being adjusted to wear, unlike linkage clutches which have to be adjusted (like mine) often. They wear according to clutch usage, the more you use it, the more it wears. Riding the clutch at high engine RPM's is their worst enemy. If it can be greased, then obviously not greasing it is a bad thing too. Clutches out of adjustment will cause them to turn constantly, just like riding the clutch does.
The U-joint is the "knuckle" that is on the end of your drive lines. Most OEM ones are sealed, but most everything that is sold as a replacement, whether OEM standard or a 4X upgrade, comes with the option of being grease-able. Lack of grease, stress (like tight articulation or heavy throttle on solid ground) and outside abuse (hitting rocks, water, dirt) does them in. Many can go for years with out issue, but 4X's, muscle cars that get driven hard, etc see the ones that fail the quickest or repeatably.
The bearing retainer is plain and simple. It retains the front main bearing on the main transmission shaft, and allows transmission fluid to lube the bearing, as well as hold it in place. Find a way to stop leaks 100% for life and you'll be a billionaire.
I'd find out if your release bearing and u-joint are grease-able, which anyone else (fellow Jeep geeks
) will likely know right away if they are. But I'm guessing they are not, at least OEM wise. If they are, grease them regularly and try to not abuse them. If not, then try to save abuse and forget about them, as there's not much else you can do. Unless you do ride the clutch, they likely just failed. Parts do that.
Another thing to think about is it would be ignorant of the tech to not fix or check for as many things as he can while in there. One reason is he gets paid for it, and second, if any related parts were to fail within a certain time frame, they'd come down on him for not doing so. So it's quite common to see numerous things repaired when maybe just one was the culprit, especially under warranty.