I have a hasquvarna 650 rtt tiller . The gear shifter shaft is seized . The transmission itself is fine it's the shaft going through the tranny body itself that's seized.

Possible shifter fork in the tranny is broken. Also inside the engine there is a little lever that pulls on a pin when shifting. That pin could be broken. Also pull in the clutch lever and try to push the bike if it moves then the clutches aren't stuck together if it doesn't move freely then its possibly a set of stuck clutch plates. That's a simple fix.

I believe up shifter shaft that goes through the transmission case is seized you may have to remove the valve body to remove the shifter shaft to clean and lubricate but sometimes you can use lubricant on the outside and it may free up the shaft,you can unhook the shift cable to prove if it is just a worn cable or seized shaft

5 speed

is it still on the bench>????????
i rebuild many

1: the bearing in the front is bad.
2: the tranny is locked, bad shifter rail, detents
3: 4th gear is not a gear, it just locks themain shaft.
so if in 4th gear and input is jammed, that means
the cluster is jammed. if the cluster jams for any reason
it will be jammed in neutral. too, because the cluster always spins.
bottom counter shaft is called cluster. to old folks.

tell me , with the lid off tranny box.
did you test all gears, by moving the collars 1 by one.?????
each gear,? if not why not.????? never skip this step or fail big time.

then test all rail detents to make sure they all work(lid off)
and never allowing 2 gears selected at once (job1)????

then put in a new shifter sheet and try all gears on the garage floor,
all assembled!
then turn input by and and shift all gears on garage floor
i even use a huge drill motor to test tranny on floor, with tape on tip
of pilot shaft. and shift all gears,

this is all basics, , never just throw it together, do the tests.
as you go.

this one is close,
http://www.fixkick.com/tranny/5speed-rebuild.html

In or under air filter cover.

there is a reason it's hard to start... how about fixing that problem instead

Best guess is that the gear for 3rd speed is seized together with it's brass bushing and the center, large transmission shaft. I don't recall which gear is for 3rd, but the transmission has two gears (2nd and 3rd speed) which have brass bushings in them. The brass bushing should spin freely on the center shaft (when in final position - sometimes they pull off the shaft tough, but spin freely when in final position, my opinion is that this is OK), and the gear should spin freely of the brass bushing.
My guess is that the 3rd speed gear, being seized to the center shaft, cannot freely idle on the center shaft, which would result in being stuck in 3rd gear.

If the tiller tines where jammed, the tranny and motor where still trying to turn and there could be a couple different parts broken. The tranny main shaft make have busted, the tranny gears could have jammed. If the motor does start, than that is a good sign. If not than the connecting rod or crank may have snapped.

I am guessing you will probably have to dismantle the transmission and see if there are any broken gears or shaft.

yes your forward lutches are goin out , time for a rebiuld or new tranny

I've seen a similar issue on other transmissions where the shifter slips out of the slots in the shift forks, either due to shifter bushing wear or just general wear on tte trans. It can usually be remedied at least temporarily by popping the shifter top off the trans and resetting the forks all back to nuetral and then reinserting the shifter. It gets jammed when two forks are trying to engage two different gear sets.
On one of the 4x4 sites, they tell you how to replace the shifter bushings, cheap fix if you are lucky.
Good luck.