need help

Im completely lost here. I have a 18 Ram 2500 cummins and currently im running a tune a local shop flashed into the truck but their are some things that need to be adjusted. The problem is where it isnt a file i can edit im having to start with a stock file and build from their.my truck has been deleted and had an upgraded valve body installed so flashing a stock tune file will not work in my truck. if i were to flash my truck the current tune will be rendered useless since my autocal isnt linked to his tool anymore and that would mean id have to try and build a similar tune file just to be able to drive my truck. how should i go about this and not end up losing the ability to drive the truck