Having it tuned for 91 octane will give you a bit more power, I am not sure on the fuel mileage. I had Justin tune mine for 93 octane and love the results. As for your thermostat I would imagine it would make a difference in power and fuel economy until you install the 180 degree t-stat.
In my opinion you should purchase the option were you get free re-tunes, have it tuned correctly for the stock t-stat, and than get a re-tune when you install the 180 degree t-stat.
I would check with Justin but I would remove 100% of TM for 2nd-3rd shift and if you truly have a shift kit than I would remove 100% for 1st and second also.