i'd almost say the tuner did a bad tune. a mild 5.0 should have no problem running 30#ers on a mild combo, with a proper tune, it should idle and drive and run like stock. i use a tweecer have 42s currently i am using N/A until i get my turbo on, 42s are WAY oversized for my N/A motor that may be making 300rwhp is that, ive managed to make my car run and drive excellent with the big injectors, and i am just a DIYer not a pro. so a shop that specializes in mustang should have no problem.
if all the sensors are new and working and the ECU is good, the EEC is TRYING to work correctly its just that something could be amiss with the tune.
i'm would bet this is an issue with the injectors and MAF and the ECU not being tuned properly for them.
you could try removing the chip and putting a stock MAF and 19s back on and see how it runs just to diagnose.
if all the sensors are new and working and the ECU is good, the EEC is TRYING to work correctly its just that something could be amiss with the tune.
i'm would bet this is an issue with the injectors and MAF and the ECU not being tuned properly for them.
you could try removing the chip and putting a stock MAF and 19s back on and see how it runs just to diagnose.