My 02,

Vehicle 1 with canned start up tune, fires right up and runs like a rock star until we hit the dyno. Vehicle II with same mods and same canned tune, blows clouds of black smoke out the tail pipes n requires significant adjustments to make it run even half decently. Why it happens, who knows but can tell you for a fact it happens more vs what some peeps think. My point, canned tune is just that, a tune that works on some but may be a nightmare on others. Whipple on a Cobra with 60lb injectors and supporting mods is a super super super common combination, have the seen the above happen on several occasions. In the same breath, recently did two similar blower fox combos, both ran like a champ on same base set up.
If it was mine, confirm everything is working as it should then have a competent tuner strap it on the rollers to see if the issues can be ironed out.