1999 Jeep Wrangler is not recognizing transponder key after battery disconnect. Starts and then dies. Does key go bad ? Or is it likely the computer ?

try resetting alarm lower drivers side window and take out keys,disconnect battery and fully charge it , when you reconnect battery alarm will go off ,put key in drivers side door and turn key all the way open and all the locked 3 times then remove key that should reset alarm.

you lost the back up RKE fobs? Remote key entry?

the operators guide covers this.
as does the FSM
and all remote RKE fob sellers on the web.

you can read the FSM.
read customer learn page, here.
i chapter
ehicleTheftSecuritySystems


http://www.jeep4x4center.com/knowledge-base/index.htm?utm_source=cj#service


you lost the back up RKE fob?
I just got my 08 and day one i made a 3rd and 4th key.
transponder.

your jeep and my JK jeep takes 2 keys good for me to make a 3rd work.
direct link
http://www.jeep4x4center.com/jeep-service-manuals/Jeep_Wrangler_TJ/1998/VehicleTheftSecuritySystems.swf#pagemode=bookmarks&toolbar=1

the rules are clear and zero slack,

Burn it

Is this vehicle a stick or and automatic? based on your write up it sponds loke your popping the clutch to get it started. If thats the case you need a starter. If not then check the following:
Battery cables off the battery and starter ,starter relay and ignition switch. These are the items in the starting system for no crank and no start.
Get Shop manual and do the appropriate testing for each.

Please refer to this solution: http://www.fixya.com/cars/t1016149-1989_jeep_cherokee

It's probably the A/C relay under the hood indeed. And your battery might have gone bad too.

It is most likely from that actually. You may need to adjust the air / fuel mixture after modding the intake. Sounds like its getting too much air.

you must program you new P C to your vehicle you'll need a scanner

You have to measure the resistance across the key and get a resistor of the same value at radio shack and jump it across the wires at the security box, this way the security system thinks the key is always inserted. We did this with 1989 firebird some years ago and it worked great.

One possible explanation for this is that the crankshaft position sensor is going bad.

Checking your fuel pressure would be a starting point.