I couldn't find Embro mufflers. Do you mean Emgos?
They're OK mufflers for the price, but you won't get the kind of performance you would from a modern premium muffler. If you're looking at the 'shorty' reverse cones, be aware that they're extremely loud.
I'm not familiar with setups on the Mikuni carbs, but in general and from my experience with CVKs in these bikes I'd say take it easy on your jet changes.
The first thing to do is get your idle and small throttle settings sorted out. That's important because if you go oversize on the main jets, you'll be able to get home with some gentle throttle!
Try the standard pilot jets first with about 2-1/2 turns (consensus setting) on the mixture screws. Run the bike on the street from an idle to high rpm with the absolute minimum of throttle opening and pay attention for misfires, weak operation and the like. If it feels weak, 'boggy' or you're getting misifres on small throttle then go up one size on the pilot jets, set the mixture screws to about 1 turn and try again.
Ideally, the operation should be smooth and the bike should feel 'eager' to run. If the small throttle operation is off, the transition to larger throttle operation won't be smooth.
Do pretty much the same for the main jets but at Wide Open Throttle. WOT response depends on the main jet sizing, so take it in small steps. Plugging in too big a set of mains can cause the bike to buck or stall when the throttle is opened and this condition will be worse when the engine is hot. Too lean jetting will cause bucking also, but it will be much more obvious when the engine is cold.
It's important remember with jetting is that a cold engine runs lean and a hot engine runs rich, so a cold misfire may disappear when the engine heats up. Likewise, a hot misfire may disappear when the engine is cold. That will help you figure which way to go on your jetting.
When you're not getting misfires (hot or cold) and the bike feels like it's running strong, then it's time for a dyno run to verify the settings and/or decide whether to adjust jet sizing.
Good luck!
Jim
