01 with no power at mid range
 

Ive got an 01 24 valve that i recently installed into a ford excursion. I bought an Optishift transmission controller to re-work the transmission for the new motor since i am running the ford 4r100. The motor runs incredibly strong everywhere except around 70 percent throttle. I tried doing a APPS reset with no luck. It did make it better, but not where it should be. The motor sat for a few months so Im trying to get some fuel and some cleaners through the injectors and have run about a half tank of fuel so far. Any ideas what my problem might be? I really appreciate any help.

Scan for codes? what apps reset procedure do you know? The one that manually resets it or that usesless disconnecting the batteries trick? Cool swap by the way, post some pictures!!!

I disconnected the batteries, and left the ignition on for almost 40 minutes. Hooked them back up and pushed the gas, then slowly let it all the way out. Started and drove, ran a little better, but still not great. The motor seems to bog right before it shifts gears. I havent put a scanner on it yet. When I reflashed the transmission, the controller came with a setting for the 7.3 powerstroke which would normally be mated to this transmission. Im wondering if the shift points might be off and need to be dropped down 100 Rpm or so. Anyone know the shift points for their auto tranny?