Manual trans is stuck in first gear - 1989 Jeep Wrangler

Try shifting the trans manually through the gears and see what happens,doesnt cost anything so,possibility valves are sticking in the valvebody after sitting so long,and manually shifting the car will force some of them to stroke in their bores unless REALLY stuck.Could also be shift solenoids.Scan for diagnostic trouble codes.A bad solenoid will have set a trouble code.Just FYI,1991 was the first year Ford went to all electronic trans,i had a 91 Sable.

so , it seems the engine does start in gear, with clutch depressed.
or cranks , brakes off, and car does not move. with clutch depressed, if yes, then the clutch is not 100% seized.
we now know the trans is in neutral (could be siezed check its Gear lub levels?)

I can not decode, stuck in gear. elaborate that.
nor "
"still stuck"
the only clue here, is
"stalls when clutch is let out."

this last statement makes me presume you depressed the clutch
then turn the key to start, it started
and when you let the clutch out, the engine stalls
does it do that rear wheels (2wd mode) ? lift driving wheels off the ground.... (these proves engine not weak)
yes, transmission is sized.
no, then it is stuck in gear.

Manual trans stuck in gear is usually a "bad thing", and may require a complete rebuild.

check if there is any trans fluid in it. If so it can't be black. shange it or fill. Hope if will work.

does the clutch push normally or is the linkage broken not disengaging clutch, and then does shifter move around or locked and wont move, loose linkage in shifter or gears are jammed inside transmission and something went, if shifter wont move at all then trans is jammed inside and needs repair.

it it an auto trans or manual trans? '
if its a auto trans: check to make sure your 2 or 4 wheel drive is not in neutral. try switching the slector or shifter around to make sure its fully engaged. sometimes they accidently slip out.
if its a manual trans: are you sure its actually going into each gear? it might be just stuck in neutral and need clutch work. those shifters have a lot of slack. probably needs a new throw out bearing or spacer to fully disengage the clutch

I suspect it's manual trans? (You didn't mention) If it's manual trans, check bushings on linkage rods at trans, yes easy fix.

THIS TRANS IS IS ELECTRONIC CONTROLED 4L60-E IF YOU HAVE THIS ONE. IF NOT THE OTHER TRANS. HAS A THROTTLE VAVLE CABLE (TV) VAVLE MAYBE STUCK OR CHECK SPEED SENSOR ON TRANS. ON TAIL SHAFT MAYBE CORRODED.SITTING 3YRS. MAYBE VAVLE STUCK IN TRANS.

I currently have the same problem, and looking at replacing the transmission wire harness. I'm hoping this will cure my problem. My volkswagon mechanic thinks so anyways.