I don't have first-hand experience with 13mm pumps and wicked fast injection cam profiles, but I'd have to assume that they will have some funky/non-stock-like running characteristics. It's possible that there is nothing wrong with the motor, pump, injectors, etc., you're simply experiencing the side-effects of running 100% race truck setup on the street. It seems that some get away with 13mm pumps with the standard Bosch quick-rate cam but you're probably running in uncharted territory for a street truck, cold weather start, truck with that new pump cam, 13mm, head, etc.
Hopefully you get it figured out and it's nothing major. We all want to see your truck perform well and succeed!