Dang tom, you treed me!
I'm not trying to be a wiseguy or put you down whatsoever, but please read on keeping that in mind ...
you're asking a very specific question about the one upgrade that is likely affected the most by all the variables that can exist in and around an engine. Whether or not an exhaust upgrade or change will perform better than another can differ vastly between nearly identically prepped engines. exhaust systems function and should be designed on intake flow in and through the head (with the flow numbers generated with EVERYTHING in place--not many bench ops are willing to rig the entire induction system at their bench) AND also for how/where the power output is desired. engine building for peak performance isn't voodoo, it's very systematic math, but without the proper knowledge and tools few people can achieve the creation of complete engine that gives the best volumetric efficiency for its displacement.
The only person really with the answer to "Which would be best for your engine" would be you after trying them all out. Of all of the tech articles I did, exhaust comparisons were always the biggest nightmare. Days on the dyno running and rerunning and watching little changes completely flop results. Yes, throwing a header on a pretty badly exhaust-restricted engine can give good to great increases for every engine in that situation. Then try another and see those increases at a different locations in the powerband--maybe more maybe less. Which is better???? Depends on what the end user wants. Change a carb and manifold and watch an equal tube header get killed by an unequal setup, or singles tubes wipe a Tri-Y only for the tri-y to have a really nice bottom end burst to them but not be able to handle the upper rpm flow levels. I've seen ugly, pitted but lovingly home hand-ported cast iron stock manifolds mop the floor with mandrel bent high dollar headers -- only because they were ideally worked to flow what that particular engine wanted.
Honestly, you're asking for info that only a rare few likely have a complete "X with Y is better than X with Z, but Y with Z is dynamite!" answer.
Now, with all that drivel written, if you have a stock headpipe and you have either increased intake flow, upped the cubes or done other work that has left the Intake/Exhaust flow ratio wanting better numbers on the exhaust side, then logically, you'd want to start by putting a bigger outlet on the exhaust (I have yet to study the heads on these to see if anything can be easily ported and whether port-matching is needed or worthwhile).
You have half your answer in that a less restrictive muffler helps, but you can also hurt performance by losing too much velocity. (going too big) Feed that gutted muffler with a larger pipe first and see what happens. Maybe then try a stepped pipe. Then add in whichever hi-po muffler tickles your fancy and try that on your stock pipe, your straight pipe and your stepped pipe.
But even before that, I'd try and find out who some of the "old school" engine or header builder names are in the racing go kart world and make a few calls. You'd be surprised at how receptive some are. Vague answers to this one on a forum are nothing to be insulted by, i bet between all the dune buggy and karting forums, (there are a lot of them too!) there's only 1/2 dozen to a dozen guys (likely race teams) who've "scienced" out all the applicable systems to their engines to find the ideal setup--and they probably guard that info like fort knox.
BTW, my bird is on its 4th variation of its 5th exhaust system --over 15 variations in 12 years.
When one asks what a bigger tire or different gear will do --lots of fast answers because it's pretty easy math. Start asking about exhaust and don't be surprised by all the crickets ...
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