I just randomly decided to check these forums finding your thread. Very interesting as my car is fucked right now as well with similar symptoms. I have an 2008 S5 which I replaced the battery with some O’Reily battery in Sept '18 ignorant to the need to program/discharge the battery to the car.
I have had intermittent MMI power surges, especially under full throttle, happened about 5 times since I installed the battery. However, right now my car feels as if its in full limp mode with anything beyond 1/4 throttle depression. Shop discovered HPFPs are not functioning electronically (they can manually turn them on, test them through VCDS, and they make pressure upon ignition, but after that nothing). Also at the same time pumps failed, my right front head light ballast was fried. We have replaced HPFPs, high pressure sensor, discharged and programmed battery, checked SAI, checked fuel for water, checked gas lines for pinches/kinks, checked wire harnesses, LPFPs…everything. We are not at replacing the ECM reprogramming it, and then reflashing the APR tune.
Been in the shop for 5 weeks now…I may ask them to do the battery to OEM next ???