I think I'm uniquely qualified to help you on this one. I owned an s2r 800 with boomtubes and currently own a 2012 M1100 evo.
First, boomtubes.
Good looking exhaust but sound can be a little raspy. In my opinion it's a bit hard to tune. If you are ok with sound halfway between a harley and a ducati you're on the right track.
You will lose some power (or specifically you won't gain much) , even after dyno tuning you might be hair above stock.
You bike will handle better. I noticed the centralized mass (or lack of) of the boomtubes immediately on the first ride.
Mark is a busy man and lead times vary. Might be a really long time before you get yours.
It was a decent exhaust overall but I missed the booming note of the ducati.
For the qd are you talking about the exbox or the high mounts? I had an exbox briefly on my S2R800 and can provide you with some input
The evo motor is pretty much to the limit of the 2v valve train. I can't emphasize how important proper fueling is so expect an ecu flash and PC-V for good operation. Even with just an exhaust mod.
If you want other options to open up the wheel
Consider shift tech. This can be run without the passenger pegs
I personally run an sc project gp m2 but that requires either the passenger pegs or in my case an evotech bracket
Here is what mine looks like. It's slightly less exposed of a wheel but a great slip on. It's loud but not too loud. Either that or my hearing has been shot by riding with boomtubes for 5 years