If the rails are aligned, it is in neutral. (unless the shift forks are bent or broken.) if you can run the engine with the clutch out in neutral, it is infact in neutral.
Two issues remain.
If it is very difficult to roll (free wheel/coast) when in neutral there is something way wrong in the final drives/bearings in the trans/final drives, or brakes.
To eliminate the brakes as an issue, loosen the housings till a 1/4" gap is visible between the housing and the tractor. This will release the brakes no matter what, but not disassemble them. If it now rolls free, (do not drive it this way!!!!!!) the brakes are a part of the problem, and need cleaning and sanding with 250 grit paper in a non directional pattern, along with the expanders being cleaned and ball ramps polished some, to make them function.
There remains the issue of the TA
Getting it out of gear is supposed to be easy. The TA clutch is supposed to release fully just after the Master clutch is released. There should be clear visible motion of the TA throwout bearing when the clutch pedal is pushed to the limit. When let out, the TA clutch Throwout bearing should just pull off of the fingers, assuring the clutch is fully engaged.
Any drag on this clutch (not releasing) will jamb the gears.
The TA assembly could be deteriorating and its bearings could be going out (info from your original post about the case moving) this could be a source of additional misalignment, and friction in the TA/transmission front input shaft.
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