A conceptual question follows- but requires recounting my [imperfect] understanding.      Or misunderstanding:

Our wonderfully crude, single-cylinder 2 stroke engine couples the ejection of exhaust with the introduction of fuel into the cylinder- the front and back door open at the same time, as it were.   Surprise-surprise, some of that fresh fuel leaves the cylinder with the exhaust gas, assisted by a related negative pressure wave- and here's where my exhaust design query comes into play.   With a properly contrived exhaust, that wave of negative pressure doesn't just pass out the exhaust exit, but is reflected back by obstructing geometry as a returning positive wave; this positive wave engages the escaping unspent fuel, driving it back into the cylinder where we want it, and simultaneously contributing to pressure in the cylinder.   Timing this negative-positive wave to the stroke cycle is why mufflers are typically at or toward the terminus of the exhaust and not affixed directly after the engine exhaust port.

Perhaps some questions should be reflexively answered by the above understanding- but, you know what they say, "when you assume, you make an ass out of yourself, a yard ornament out of your bike, and Batman will justly dope slap you for not asking", so-

Those cool kids who dispense with their muffler, side venting the pipe somewhere between the rear wheel and transmission case, are throwing away fuel and power, aren't they?   Kinda the opposite of a supercharger?

What options do we have for ascertaining if positive exhaust pressure is both adequate and well timed?  

What options, good or better, do we have for tuning an exhaust to deliver the needed pressure at the ideal moment?   Exhaust length trial-and-error is consumptive of time an treasure- is there some sort of moveable baffle employed at the muffler front to adjust the reflection point and flow/pressure?

I suspect the path to seemingly simplistic design solutions is typically anything but simple.

I'll attach a picture to trap you in the post long enough to reflect.

MATH !

I have to say, I'm amazed at how "overanalyzed" this seemingly cheap, POS, under powered LS650 is on here.  And I don't mean that in a bad way!!!  

There are a lot of really smart people on here and we all love the LS.  I'm just amazed how the bike inspires so many people in so many different ways.

I don't know very much about two stroke exhausts. But I do remember many years ago, in England,  I owned a Zundapp 201s 200 cc two stroke bike. It was very quiet relatively speaking and for its time high performance.
I felt that if I took off the HUGE silencer it would surely go faster. WRONG!
The bike dropped from 70 MPH to 60 MPH instantly, on top of which, the noise was incredible.

Those German engineers certainly knew what they were doing when it came to designing a two stroke exhaust system.

I have had EXACTLY the same idea for some time but I am thankful to batman for explaining that this is primarily a two stroke thing. Now I can keep my Silvertail exhaust and focus on other parts of the bike instead.

IslandRoad Your expectations for the intake may also be too low. Gains there can be higher than that of the exhaust . After market carbs and work like DBM did to the intake passage ( reshaping with filler etc. ) I've done neither of those,  but have gained 3 to 4 hp by adding 6"of pvc pipe between my rubber carb tunnel and air filter (intake tuning).