One possibility that comes to mind is the O2 sensor. Sounds like it is running alright in open loop mode, but when it goes to closed loop as it warms up it starts taking info from the sensors and if the sensor is crap it will run like it.

When it is warm, how does it do on wide open throttle? That is another circumstance that is open loop. If it takes off fine when you floor it but runs crappy the rest of the time when warm it points to a sensor problem.

Steve Carlson - 95 Trooper LS expo rig
Serenity now!