When I had a '93 Trooper, it started to happen to me after my alternator
went of the flitz (must have spiked the electrical system)...shortly after
my starter went (what a coincidence).  

Back to your problem though... It seems as though mine did it when it was
damp and cold out (usually on startup)...It had nothing to do with the
transmission, (at least on mine) and everything to do with an electrical
problem (when damp out, after starting the vehicle, it seemed to sputter a
bit (thus if you started driving, the trasmission computer thinks you are
having a problem with the transmission and puts it into "limp" mode-
straight 3rd gear).    

If you have a repair manual, it may have something in there on how to read
the codes (without a code reader)  I think I had to short 2 pins together
on the plug on the Drivers side under the dash, then the light would flash
the code back to me- came back as some transmission solenoid.  I didn't
think that was the case because it would only happen on a rough idle after
starting.

I read somewhere that many electrical problems on the Troopers happed from
oil "pooling" in the spark plug wells- IMO due to a manufacuring defect
that ISUZU is not taking care of, but that's another issue.  Try removing
all of your sparkplugs and see if any are coated in oil (3 out of 6 of
mine actually were coated on the outside of the plug- where the boot plugs
on to them)  Isuzu does sell a new spark plug wire set which is suppose to
stop the "pooling" of oil by sealing the spark plug well better with a
revised boot- I think the set was $60 or so from the dealer, but make sure
you get them from the dealer, as aftermarket may not be revised to current
Isuzu specs.  also replace your plugs then and be sure to coat the wires
with dielectric grease (lots) otherwise you will not be able to get the
wires out without ripping them.

Hope this helps.

Often when this happens the car will act like it went into neutral.
Quickly turning the engine on and off will likely fix the problem (right
then). The following was posted by a service manager (accidentally
snipped his name) some time back.  The question comes up from time to
time.

We did a complete service on ours (flush and change) and replaced the
battery and the problem went away.  In our case the battery was bought
in an emergency while on vacation and was way to small which exacerbated
the alternator problem (we suspect).  From what I remember some
alternators have bad regulators and that causes a spike in voltage which
causes the computer to get involved.  Try the on/off idea and if it
works perhaps you can find someone to check the alternator to see if it
is spiking.  Hope this helps.

Frank

If you are going to take the alternator off and have it checked at a shop,
your best bet then, would be to replace the whole darn thing as the
regulator is built into the alternator before other quirky problems start.
Also by your battery being dead 2 x and your alternator working extra
hard to recharge, it's possible you may have a bad cell in the battery,
and now the alternator may have a problem with one of the diodes in the
rectifier within the alternator... bottom line, I would start with a new
alternator and battery.  The interference on the radio may be caused by a
bad charging circuit (should be filtered by the battery though) try the
replacement of both and see if it goes away.  If you can do the work
yourself, it should be under $200 for a rebuilt alternator and battery.

I have a 93 Trooper and had sort of the same problem. It would go into
limp mode until I turned it off and then on again. This would cure it
for a while. I put two or three batteries in it and this worked for a
while also. Finally took it to someone who new what the heck he was
doing(NOT THE ISUZU DEALER).He drove it home for about a week with all
his meters hooked up to it. Turns out it was the regulater on the
alternator that was going bad and sending a surge to the computer!It
was spiking up to 18 volts and the computer was seeing this and went
into "limp". Since having it replaced last year have not had one bit
of problem......................knock on wood................Jim

Well I did replace the alternator but no luck.  Trans light is still coming
on. I did observe another pattern which was that the light only comes on
after the trans upshifts from 3 to 4 gear.  Any other idea...I'm about to
give it in and take it to a tranny shop...