I did it once with an H&S tuner. Flashed the normal tune then put it in recovery mode and forced a manual flash on it from the canned files on the card.
If you didn't flush or replace all the fuel lines prior to installing the new fuel pump, that trash probably wiped out all the new components after it ran for a short time.
Correct. Don't forget to replace the trans cooler on the frame rail at the same time. (one thing i havent tried yet but would love to experiment is the TC from a current High Output truck. I hear that is the main difference in the power rating.)