I had a problem similar to your's. MH 1997 Engine:Cummins M-11. trans. Allison HD4060R.
Allison dealer shop said NO fault code, go see Cummins/Freightliner dealer.
Result: lots of false code on engine ECM (electronic control module). ECM shot need new one.
Put new one in ($3800.00) all problems solved. Rene