Hmmmmm, was the knocking that you first heard when you programmed it with the Hypertech detonation (aka spark knock)? I assume the Hypertech works the same as other tuners by advancing the timing. What grade of fuel have you been running in it? Most tuners require a higher octane fuel after tuning. Advanced timing plus too low octane fuel and/or anything more than light pulling or hauling would definitely cause detonation. I know severe detonation can lead to holes where there was not holes before but I don't know about bearing wear/failure. Maybe light detenation of a long period of time?
Best I can find, P127E is a fault between the TIPM and the fuel pump. Here's some good info on it.