It starts off in 2nd gear if I'm in "D". It WILL go into 1st and accelerate great IF I have the selector in "1", and then manually upshift once I accelerate.

Fluid is at correct level and nice and red.
I adjusted the kickdown linkage, but didn't help.
98 Jeep Wrangler - Automatic Trans - 92,ooo miles.

Any ideas?

will it shift into third or forth? some jeeps also had a problem witt the TPS, i don't know if they fixed in by 98, or if it would cause this problem.

any SES light?

Yes, it will upshift into 3rd okay (it's only a 3 speed) and it will downshift to 2 and sometimes even 1, but I really have to mash the pedal.

It just won't start off in 1st gear while in "D". I'm totally stumped.

Hooked up an ODB-II, and no codes present or stored.

Has it always done this, or is this something new?
Some automatics - like Mercedes - function exactly as you describe, although if you floor it from a standing stop, they will give you first gear. Otherwise they start out in second.

I just bought the Jeep, I don't know the history of it. It's only a 3 speed automatic, so 1st gear is desperately needed.

Someone I talked to said the computer might be sending the trans bad data, like it's telling the trans that the car is "moving" and not as stop, as thus it telling the trans that it should not be in 1st gear. He said I should look into the "Secondary ECU" for the trans.

Can anyone explain how this 2nd ECU works (if I even have one) ?

I just bought the Jeep, I don't know the history of it. It's only a 3 speed automatic, so 1st gear is desperately needed.
Uh......are you sure its a 3 speed? It should be an Aisin Warner 4 spd automatic overdrive. There might be an overdrive button somewhere to give you 4th gear.
Still, these trans were electronic shift and you are on the right track. Try posting on the Jeep subforum at AF or try jeepsunlimited.com for more answers.