Last time I checked, tuning both cylinders is a mandatory prerequisite for a proper tune. And the other pearl of wisdom: I am waiting well over 2000 miles before I take my 08 SERK to the tuner. My humble logic is simple: the stress factor that your engine goes through during a dyno run is tremendous. Why take your new 110" before it is fully broken in through the torture? The easy on the new engine dyno makes sense. Checking the techs work later on, makes sense as well. Pulling 6th gear WTO for a variable degree of accuracy just to verify how anemic the factory settings are, is just too risky. Until it's ready, of course...
Yes on tune after 2000 miles or more.
Yes on both cylinders tuned...Of course.
Yes on your assumption the temps will be better after tuning.
Yes on your thinking because you obviously have a great taste in Motorcycles, how bad could the rest of your thoughts be?
No on worrying about bluing. Destiny. Get some blu boy or blu off or something if it bothers you any further.
No way to do a quick study of tuning in my opinion. It is an art form of sort: a technical art form. The results can be as good as Monet or Leonardo DiVinci, or the opposite. It is an ongoing study with many variables and techy tricks that never seem to end due to all of the endless products we purchase. To gain your trust would be the best thing a tuner could do. Then develop a relationship. It works better when you get to know them.
Mike K.
kona76