I'll put it to you like this on the 05/06 gsxr1000 muffler, and how restrictive it may or may not be.
I have owned gsxr1'ks, and ridden every generation since buying my first one new in 02.
In 05, two of my friends bought new 05's.
In 06, another 2 bought 06's.
I rode all of them Alot.
Several thousand miles combined.
And several dozen miles of wheelies, probably a couple hundred.
Real wheelies, 10-11 o'clock, balanced, quarter mile, mile, whatever.
I say all of this because; I rode all 4 of the 05/06's since new, with stock exhaust, and later, 3 with full Yoshimuras, and one with a full Akrpovic.
With stock exhaust, 40-45mph-70mph wheelies were easy.
Once the stock butterfly valves in the factory midpipe had the 2 servo cables removed, then spring held it in it's most open position(like the Bking too).
The extra gain in flow made a very noticeable power gain.
Acceleration was much more agressive(fortunately), but this meant 1st gear wheelies wanted to rocket to 85mph+(speedometer).
Throttle position and overall control needed to adust to the powercurve change.
The butterfly valve does it's job very well, which is to smooth the power delivery.
With it open, the throttle response was basically the same as the aftermarket full exhausts were later.
Not to say that the full exhausts didn't perform better than the open-butterfly stock pipes, but rather that the butterfly made the biggest difference in performance, not the header...not the muffler.
Obviously the butterfly is not an issue here.
The stock titanium muffler, is 2 or 3 chambers(can't remember, I'll have to look).
It is designed for a 160-165hp 1000cc engine, but that muffler could likely flow a few more hp too.
Is the 05/06 stock muffler sucking hp from a gen3 with a high flow header?
Probably a couple.
Could you notice it?
Probably, at least in a few spots in the rev range.
Is it a big deal?
Nope.
You like the looks and sound(I do too), and I think that's what counts.
Maybe that small exhaust restriction gives you back a little mid or even low rpm power, vs a high flow muffler for peak hp.
I prefer useable street power anymore.
Don't get me wrong either, I love to top out gears, even 6th...just a rare occasion anymore, meh, been-there, done-that, the mood has to strike.
If I was going for top speed I'de have an exhaust suited for that.
That old 05/06 muffler looks like it could've came on the gen3.
Looking foward to a sound clip.