How loud is this sound? A broken tooth is pretty noticeable. I would think some metal would have come out of there when you drained it if a tooth broke but it could still be laying in the case. You might try pulling the top off and draining it (again) and see if you can spot anything wrong. Drop a magnet down in there and do some magnet fishing. If you don't find anything you might try jacking up the rear end and jack stands. Slide it into first gear by hand and see what it sounds like with the shifter top off. You can run the trans for a little while with it drained Cover the trans with something, so it doesn't fling gear oil all over the place. Just don't lock it into two gears at the same time, that could break something, it locks the trans up solid so it cannot turn.
Right now, I have three 1948 Ford 8N tractor projects. I buy good ones cheap with problems. I'm going to help each grandkid restore one, there just little guys but they love tractors. Why not brain wash them into being vintage Ford guys at the same time. I have one that the guy was discing in second gear. All he did was come to a stop and put it in first gear and the trans locked up and it will not move. Stalls the engine the second you engage the clutch. He pulled the trans cover and tried prying the gears back into neutral and they won't move. I paid $500.00 for it, good tires, new battery, alternator conversion, runs great as long as the clutch is held in. I have not researched it yet. Th owner said there is something that breaks in there requiring the tractor to be split into two halves to repair it which isn't that bad of a job. I've replaced some clutched on those 8Ns before. I bought another one for $700 that is a real good tractor. The guy replaced a leaking head gasket and then it wouldn't start afterwards. He replaced everything trying to figure it out and then got so mad he bought a new $40,000.00 Kubota. It has a distributer like an Early Ford with the coil on top of it. When he put the coil back on, he bent that wound wire coming out of the bottom coil and grounded it out. That was an easy fix.