1. The suspension is barely tuned and if I'm not mistaken it is SOFTER than default in the front in terms of spring rate, sits much lower than stock, and is on R4 tires. It would not surprise me if the undercarriage scrubs quite badly at the 'Ring and it also would not surprise me any if the suspension spends almost all of its time on the bumpstops.
2. The differential is stock as a rock and the car has late-stage AIDS. Not only is the traction control rating excessive even for a 1960s behemoth and will limit acceleration, the ASM will ultimately limit cornering prowess (although it may help hide some of the issues caused by the suspension) and consistency.
So really, you've done nearly everything the exact reverse of what you should've. Racing tires always dictate a need for stiffer suspension just to control body motion during the more sudden, higher g-force movements caused by the increased grip (this applies to acceleration and braking as well as cornering... Stiffening may slightly harm forward bite on acceleration but it will help braking greatly and prevent the car from shifting its COG as awfully under acceleration). Instead, you've taken a suspension that already feels far too soft on S3 tires and softened it further (although the bumped up sway bars may limit body roll to an extent the issue is still there).