1. She is running really lean and needs to be ridden so the ECM can learn new AFV's with the recently installed fuell hungry open exhaust. I'm going to say she would like 114f/105r.
2. She is running really lean and needs a proper tune to satisfy the recently installed fuell hungry open exhaust. +1 to 1_mike
3. Somethings is jacked-up. Its under warranty. Take it to the dealer.
Matt: Have you changed the ECM map for the exhaust change? The exhaust change could be making the headers glow.
From what you described about it's starting/ running, it's very similar to a friend that installed a Jardine without any map changes.
You really need to look into this before you run it much more. BTW glowing headers like that do not always mean you are running lean. If you are very rich you could be burning the excess fuel outside the combustion chamber in the headers. That would really make them GLOW.