A903 No Neutral

Did you try the brakes while it was idling in neutral?
If its on stands, engine off. In neutral crawl under and and see if you can rotate driveshaft by hand. Linkage may need some work.
^ What Trailbeast said. It might be fine, not really putting power out the output, just fluid flowing.
If the brakes stall the engine in neutral, or the brakes cannot stop the wheels from turning, then you have a problem.
If the trans goes thru all the shift positions, and letting out the clutch in EACH GEAR, does NOT stall the engine, then at least the forks ain't broken. But my guess is that you will find a stick position that stalls the engine, due to it's being in two gears at once, due to a broken shift fork.
If you cannot get the car to back up; badaboom.
903s are top-loaders so the trans would have to come down.

In neutral, with foot off the pedal, and engine idling; the crank is spinning EVERYTHING in the trans except those parts which are splined to the output shaft, which is held stationary by the tires being on the ground. As soon as the rear wheels come off the ground, gear oil will, (as mentioned) tend to act like a fluid coupling and the tires will start to spin, or if an open diff, at least one will spin, but at double-speed, due to the 2:1 differential ratio. But if the brakes will not stop this action, then, more is driving the wheels than just the fluid; and so it's time for a visual inspection. It may be that one of the gears is, or is nearly, seized to the mainshaft; or a fork is broken, leaving it full-time in that gear, or a synchronizer is stuck or dragging. The shifter will still work perfectly. But letting the clutch out,with the engine running, in any other gear than the affected one will result in a stall.
That 903 has funky 50s technology inverted synchronizers with floating parts, and a non-synchronized first/reverse gear. The parts were just barely adequate for the job in their original application. Back in the late 70s, I rebuilt hundreds of those, sometimes 8 or more a day. Farmers used them for all kinds of applications other than their intended applications. Interesting anecdote,lol.
I guess this got missed, as he said "the entire brake system is torn apart due to me preparing to change everything from the master cylinder back, all fluids changed except diff."

Which means to me he is seeing bare axles turning, and no brakes to stop them.
Automatics and manuals both can do this in neutral.
In park an automatic doesn't do this because the output shaft of the trans is physically locked.
Wow! Thank you guys for all the replies and knowledge.
I went to the shop, wedged the axles with a bar to keep them from spinning, started the car, and hopped out to check out how much force was being sent to the rear end. Turns out you guys were correct, they will just spin when there isn't anything holding them, like tires on the ground. I unwedged the axle, it started spinning with the driveline, but I could stop it with just my hand.
Thank you guys so, so much. I was seriously worried about either a linkage issue, or something wonky in the trans. You all set my mind at ease figuring this out. I can't believe how this car has challenged me every step of the way, but I know it's worth it and a great learning experience.
Thanks again!!