luis,
do you have the MCFA Tier 1 diagnostic program?
you will have better luck diagnosing the truck and fixing it with this.
These Tier 1 trucks with that ECM with the vacum hose (MAF Sensor) were difficult to troubleshoot without the program.
There are many service bulletins on this system about this very issue with this setup. MCFA made many changes to the system after it first came out so you will have to verify exactly what components are on it and then get the correct diagnostic and repair guide to troubleshoot it and repair it.

There is a check valve inline with a vacuum hose that plugs into the air inlet hose that can clog up, make sure its clear and working properly.
Also the engine dwell setting can affect how the truck runs and only can be set using the program.
Plus calibrating the PPS to the TPS can be only done effectively using this program. It can be done by using a VOM but is alot more difficult.
Also make sure the mixer is clean and the diaphragm is seating properly inside the mixer. Pay close attention to the little bullet and seat in the center of the diaphragm. The dwell adjusting screw is behind a small expansion plug on the side of the mixer and uses a small Allen wrench to adjust.
You will need the proper documentation to check it out and verify the settings and adjust it as needed to get it set correctly.

good luck with this