So for starters I'm not a trans specialist, but I have dealt with a handful of t-5's and specifically this problem. Also, with a press, a gear puller and a bearing splitter and some pipe you can pretty much get everything done. Lot's of youtube vids about this, just watch a couple and see what you think.
Anyway the loose bearings between the back of the input shaft and the tip of the mainshaft starve when fluid is low, they wear down the tip of the shaft or it'll be pitted. Also, check your input shaft play, for some reason almost all of them I've looked at off craigslist have been jacked with, lot's of input play and/or missing shims in the bearing retainer. It's just like any transmission auto or not, your endplay needs to be right, not more not less.
So, in the past I begged the guys at standard gear to sell me a good mainshaft, but that has dried up. I was told you can have them either welded or sleeved, but I haven't personally had this process done. Sounds like standard machine shop protocol so I'd expect good results. I have also heard about converting to the cobra tapered roller bearing, but I have no idea where you get those parts affordably.
I have a t-5 in my car now that has always been a little noisy, but I drove the fox body it was in for a while and never noticed anything. It's tough to explain relative noise on the internet, but this one is more like...yeah there is very little between me and that transmission. I have driven M5OD's that did sound like superchargers, to the point where people would look at you in parking lots. Take a real close listen at :40, you'll hear that t5 through a couple of gears. Compare that to yours, and I have many miles on this trans with no change in noise. Not saying it doesn't need repair...but I'll need to hear a lot more before I address it. I had to swap input shafts on this trans and I can't remember what the mainshaft looked like, but I would think if it looked bad I would have caught it but who knows. The second vid is just a teardown vid of the t5 so you can gauge your skills.
quickdrive.MP4 - YouTube
T-5 Borg Warner T5 Five Speed tear down disassembly Episode137 Autorestomod - YouTube