The 6.6, though new for GM, is a great engine and the 6L90 is about as robust and reliable as you can get. A 10 speed (ala Ford-GM joint venture) would really make it shine.
Interested in following along your build.
Won't happen for some time, but am looking at GM 2500/3500 with short vs long bed double cab for a flatbed build. Shame the double cab short bed is not offered with the 3500.
The factory bed delete is a $1200 credit but as you mentioned, you miss out on a number of options if you choose that route. Furthermore, if you're not planning on upgrading tires/wheels (the 18s are already 33") you miss out on the 'free spare' with optioning the standard bed.
A flatbed...
Not to be political, but election is over one way or the other - we'll be returning to normal far sooner than later. Eg. already articles in the 'news' suggesting indoor concerts may return, aspirin may be a treatment, etc. I suspect prices in this area will remain high for some time though...