The cummins will eat or any diesel will eat transmissions if you bump the fueling pressure with a edge or other product to enhance the performance. Change the high pressure valve in the trans. and replace the shaft with a custom shaft to extend the life of the trans. Sounds like you have a faulty high pressure valve or clogged high pressure valve in the trans. 900 ft lbs of torque will do damage. The simple edge plug in will give you a number close to 900. A good trans man is a good friend when building up a cummins....LOL A nice 250 wet shot will put you in the 11's at the track
I have heard the cruise control module is a faulty gremlin causing a similar "lack of pedal" you mentioned above. do a google search for turbo diesel register .org and join.....many fine men on this site, with lots of knowledge of the cummins 5.9