Just replaced my engine in my 95'. Complete re-manufactured long block, almost every new part i could throw at it. only parts reused from old engine were, intake and exhaust and distributor. Set the timing according to the chilton manual, on initial start up it will idle smooth. Increase the rpm and it will sputter and not want to increase rpm. i shut the engine off, wait a few seconds and restart and the engine will run like there isnt a thing wrong. could i have set the timing too far off and the engine management cant compensate?

 

I'd suggest cleaning the IAL, checking the TPS and the power to it, and the CPS are sometimes known for erratic behaviour before they quit working.
*I don't know about setting the timing, other than the dist. should be installed properly.. then the PCM controls when it fires based on other sensors.

 

Base timing is controlled by the computer.

I'd verify that throttle position sensor for starters.....