Drain the transmission fluid, take the drivers wheel of and remove the nine 10mm headed (m6) bolts that hold the cap on the end of the transmission.
You will see three shift rods and some gears. Use pliers, vice grips ... to move the shift rods until there all in the neutral position and you can move the shifter freely inside the car, go through all the gears, if all is OK then clean/apply gasket maker, reinstall the cap.
Use new gear oil and change the plastic bushings in the shift rod assembly (12$ from the dealership).
You should be fine.
If metal bits come out with the fluid then the transmission is FUBAR, but it sound like the shift rods are out of alignment or the shift gate could have come loose.
If you need a new transmission one from an 88-92 mx6 gt or 626 GT will also bolt up.
Posting your location might help you find one in your area.
If you do get another transmission, I would be interested in buying the diff or just the pinion gears from it if there still good and you feel like pulling it or them.
If you need any help or want to take the next piece of housing off the transmission and check the shift gate while the transmissions is still on the car pm me and I will walk you through it or post in the first gen section.
The clutch should have nothing to do with the transmission being stuck in gear, especially if you cant get it to shift with the engine off.
The only way it could cause this is if the clutch wasn't installed properly or out of spec or the slave wasn't working properly and the gears ground on every shift finally causing the transmission to fail or he whacked the diff when installing the hangar baring shaft so hard that it shatered the diff pinion.
You would have noticed these things right away when driving it after the repair.
I think it might just be in second gear but the shifter ball (inside the transmission) managed to slide out of second without dissingauging 2nd gear firts.
Is the shifter still in the position of second gear or does it feel like it's hovering in neutral between 3rd and 5th?
You should start by checking the transmission fluid, get a clean pan and drain it, check it for metal bits...
I know this is an old thread, but I thought I'd share my Experience with this situation.
I recently acquired a 90 Probe GT with the same problem, the guy I bought it from told me that he had a new clutch installed 2 weeks prior to the tranny getting stuck in second.
My initial plan was just to buy a $650 MX6 GT parts car, but the I came across this thread.
I drained the Fluid no metal bits... Exposed the Gears & rods & was taken aback, My brother in law said that it looked as if the tranny had recently been rebuilt, so he had me sit in the car, press the clutch & move the shifter, it was roaming out of gear & wouldn't go into any of the gears, He took a Rubber mallot & lightly tapped the rods while i moved the shifter back & forth & just like that i had fourth gear then 5th then all. We slapped it all together & its been smooth shifting ever since.
i have an 89pgt with the same problem, drained gear oil and it was brand new, filled with new ATF and removed the 3 bolts under the transmission where springs and balls fall out....its supposed to reset the shifts, but it didnt , problem still there...i was just going to replace it...but maybe i'll mess with it some more and see
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