Edited - assuming the gear whine is coming from up front in the trans tunnel and not out back where the axle is ------
I just rebuilt my TR3650 and didn't do the job as well as I could have. Before disassembly the end play on the input shaft, output shaft, and counter shaft seemed perfect, no wiggle or play at all. The bearings and bearing cups looked great with absolutely no signs of wear so I reused them and the shims. (I'm on a budget)
Getting the trans back together and the final step of sliding the case over the output shaft/counter shaft is a bitch. So much so I didn't wanna do it twice. Well I had slight wiggle/end play on the counter shaft after I got it on. Now I got gear whine or bearing noise. I should have taken back apart and put more shims until end play was good. Basically the same scenario as setting up a ring/pinion and backlash.
I know my problem is the counter shaft and you can do this test. At rest in neutral with the clutch engaged NOTHING in the transmission would be spinning, no noise at all.
Let clutch out while still in neutral and the input shaft and counter shaft will start spinning same RPM as the motor. Also the gears on the output shaft will start spinning on their needle bearings; but none are locked/engaged because you are in neutral. If the gear whine starts as soon as you let the clutch out, it's likely the bearing on the counter shaft or input shaft. Put it in 1st gear and drive away. If the gear whine starts as soon as you start rolling its probably something output shaft related because its directly connected to driveshaft. If it only happens while you're in a specific gear (like second) it might be the needle bearings on that gear or the teeth on the gear are slipping on the synchro hub.
Only way to really tell is take the trans apart and inspect for damage. There are threads on here (search for TR3650 rebuild) and some you tube videos as well.