Allison 2000 CA Conversions Trans in 2003 Ford 7.3 Excursion

Have a buddy who purchased an Excursion with a ton of mods, one of those mods being an Allison 6 speed swap. 1000 or 2000 not sure yet. It shifts so bad its horrible to drive. I have tuned/built many Allisons (and all the other autos) Am I able to access/tune this beast with my V2/EFI Live or will it require something specific?
It appears by the 10-12 ECM Codes that they simply ripped out the 4R100 and did not do anything in the Ford ECM to tell it that its transmission is flat out missing.. so its pissed off at the world. The truck has 70k in mods to the engine, tuned by Swamp "something" diesels and it hauls azz. What I think / feel is happening is the Allison TCM does not talk to the Ford ECM so they are both just kinda doing whatever the **@ they want. Full line pressure, lockup in 2nd at low speed, slams each gear like a bus. If I can get to the Allison I can tune it and make it a TON better. but..... can I?
Thanks peeps,
-RM

First off you are gonna want to flash a 7.3L ford strategy with a manual trans that will get rid off all the data the PCM is expecting for trans range sensor. Another option maybe to link the Allison external or internal rannge sensor to the Ford PCM they used similar signals with there transmissions. Depending on what Allison TCM was used I'm sure you will be able to calibrate it depending on if its a locked unit or not it being a swap you are gonna have to try a read. If you need some help just reach out and I'm sure you can get it better than where it is now. If the PCM on the ford side was not modified to the new transmission there is a chance its getting all kinds of messages on the dash and it maybe hindering some of the engine performance kind of like a safe mode. You would want to fix the engine calibration to better suit the Allison and this should help with everything moving forward.