I recently got given a manual 86 4x4 pickup with a 22re and w 56 Transmission. It’s got 360k on it I don’t know past maintenance it was from a distant family member. Today I was dropping the transmission and decided to drain the gear oil and I noticed some shimmering. Upon looking closer I noticed some bigger hard chunks that weren’t magnetic. I’m not sure where I should go from here I was gonna flush it out with a few qts of gear oil and put the new clutch on and see how it handles. If it ends up needing a new transmission since it has such high mileage would it be worth putting the money into a new transmission? The engine is running strong and the transmission was slipping but wasn’t too bad. I’m 18 this is my first rig I’m just trying to set my self up for the future and don’t know what direction to go

 

Far and away the most common failure on that transmission will be the countershaft bearings. The hallmark of countershaft bearings going down hill is noise in every gear (but most noticeable in 3rd/5th) that goes away in 4th gear. If someone gave me a used W56 that had no apparent issues (like what you got) I'd still take it apart and replace the bearings.
The transmission is fairly easy to take apart. That said, having a repair manual is pretty essential. Once you get it apart you can inspect the gears and synchro's. Fortunately, both are pretty durable.
Toyota has specialized tools for the job, but can be easily worked around with some improvisation.
Good quality bearing kits with Japanese (koyo/Naichi) bearings are priced fairly. Marlin Crawler often has good prices.

The worst part of the job is simply pulling the trans/transfer assembly. That is one heavy unit. I've done it solo, but a floor jack and a second pair of hands is very helpful. So if you get the trans out to replace the clutch you definitely don't want to put it back in without opening it up. Something HAS started to failed. That's a given. Assuming right now it's bearings you need to replace before it gets so bad that gears start clashing from not meshing properly. That would change things drastically.

The top two bolts holding the bellhousing to the engine aren't a picnic. Having about 3 feet of extensions on your socket will make it easier.