2009 Audi A6 3.0T APR Stage 2 ECU Tune & Supercharger Pulley Upgrade, 72k miles, no extended warranty

Over the last few months, my car would slam into second or third gear really hard if I punch the accelerator. Usually would happen in sport mode when approaching a slowdown situation anywhere from 25 to 40 mph then light turns green and punching accelerator. Continued to worsen and was advised to have transmission looked at. Took it to a local shop that was highly recommended and they determined it is most likely a valve body issue. They replaced valve body and mentioned something about the solenoids needing work. They ordered an upgraded kit and had to send car to Audi dealership to get programming done. Received car back from Audi and programming had not been done so they had to send it back again. Total cost for everything was around $2000. I have been driving for just over a week and the slamming into gears has been getting worse and now extends into the third gear as well. Yesterday, it slammed into gear and I got notice of "gearbox malfunction, you can continue to drive with limited capability". Drove to friends house and car never shifted out of second gear. Turn car off and restarted, no more warning but seem to be driving a little worse. Called the shop and they told me to bring it in Monday.

I've seen this indicated throughout the forums but usually with S4. Have not come across it with the A6. Have heard TCM and mechatronics mentioned. I'm a moron with this stuff and have no idea what any of it means. Anyone have experience with this? Bluebook on my car is down to $10,000. Wondering if this is common problem and what fix usually costs. Thanks!