Sorry I did not finish some thoughts. I started replying just before dinner and had to run.
If you have other questions about the gearing, send me a PM or reply here again.
On the rust. When I got my truck and drained the tranny oil the first time I was alarmed. Lots of metal. I pulled the side access plate and there was a rust line about ½ way up the plate. And at some point almost everything below that line got some rust. There’s a good chance my tranny was submerged at some point and took in water. Or it could have sat out like yours and gotten swapped in.
Another problem with not having a seal on the input shaft is that it also lets water in! This is true when submerged or when day to day changes in the environment, e.g. pressure, humidity, temperature. From time to time there is a burp and water gets in that housing and quickly turns to rust. If it sits out in the rain it will accelerate this phenomenon and get lost of water in there, that again becomes rust.
Back to my tranny. I think it got lots of water in it at some point and when operated the rust getting chewed off the gears made a mess of it. The first change of gear oil I did was a flush. From then to the second it was better and I did it at a close interval. The amount of metal coming out decreased drastically.
Recommendations:
1) Clean the rust, especially on the gear mating surfaces best you can. You can get steel wool in sheets that works well for that sort of thing (rather than the spun stuff that flakes away all the time)
2) Clean anything else left over. Set it on its’ side and blow out with compressed air. Set it in the natural position and flush out with diesel and let it dry
3) Install a magnetic plug for both the fill and drain. This allows you to pull the fill from time to time to clean off the metal and get a chip count without draining it (keep a log book and\or take good pics with the date). This is the same concept used with helicopters. Go NAVY! Also, consider replacing all of the seals. Erik’s has the whole kit for $40
4) Consider adding an input seal while you have it out. Mush easier to do so now…
5) When you do run it, do so for a limited time (maybe 50 miles) and drain the oil. This will allow the worst of it to get flushed without exacerbating wear unnecessarily. Watch it closely and change the oil if you think it should be changed or at increasing intervals, say 50, 150, 500, etc. Eventually you will have “normal” oil change intervals