What brand was the crate engine the first time? Sounds like you just got a bad build to me. BUT, the driving home running rough gets my attention, can the TBI fuel pressure regulator fail wide open? The reason I ask is some ford regulators can, and if you continue to drive it will hydro-lock the motor. I rebuilt one ford v6 years ago that had hydro-locked on the highway, the damage inside was incredible, all we reused was the block and heads. Just wondering if yours was getting close enough to beat the lower end to death without locking up yet? What did the oil look like?