So what I ended up doing last year was a normal 1040X through TurboTax where the only thing I changed was my new non-deductible contribution info. That resulted in a new 8606 with the correct numbers. On the 1040X itself, the only change was that I added a brief summary of why I was sending in the 1040X (to submit an amended 8606). I mailed in only the 1040X and the updated 8606. I just verified through the IRS "Where's my amended return" that it was received, accepted and processed last January.
