Tank5280

I have a 98 24 valve, a few months back I was using a bank tuner on the truck. During the process of downloading new files to the truck, the tuner lost connection and didn't finish the tune. Witch fried both ecm and pcm. I have installed remanufactured ecm/pcm that have been programmed to my vin. Now the truck starts and runs but now throws a fault in companion module code and thats the only code it shows. My tachometer works for about 5 sec when I start the engine, then the tach drops and the engine rpms ramp up a little bit and the check engine light comes on. If the truck is in drive it will shift gears and move but it has zero power and i have to floor it to even go past 20 mph and the rpms raise but the motor stalls out. I think that its not getting enough fuel. The truck has a fass fuel system that is good and works. But I think the vp44 isn't turning on because the modules are not seeing the engine rpms, so the vp44 doesn't know how much fuel to put into the motor for the load. Are the ecm and or the pcm faulty still? The cam sensor has been replaced and the apps has been changed and the crank sensor has been changed. I have no idea what to look for or how to fix this issue.
Thanks, nick