Some questions on some work... i.e. removing headers on m796 etc...

[thought]

hey guys... decided to do some last minute winter mods before the spring hits.  got a friend of mine to let me borrow his garage to do all the work.  i was going to wait till i passed the 1st 600 mile inspection, but then i realized that would mean a good amount of downtime during the riding season.  and after seeing how hot the bike gets in cold weather, i want to do as much as i can to reduce the heat before the summer.

going to be putting in cf termi slip ons, caswell'ing the tank, putting on a evotech, and sending the headers out to be ceramic coated...  and my main question is about the headers.

i've dl'ed the m696 shop manual (cant find the m796 or 1100 shop manual anywhere)...  and i'm basing what i'll be doing on that.  is there any diff in the procedure for the m796?  what i'm worried about is that exhaust flapper.  is it pretty obvious what to do about it during the removal?  and if i'm fitting the termi's in... do i have to even bother reconnecting it?  from what i understand, getting the ecu in removes the need for it?

thanks for any help on this