Bob, I recommend you run carbs in as-delivered configuration without changing anything. Muffler-only upgrade does NOT require any jetting changes. It's full-exhaust that changes flow significantly enough to require it.
As with everything else, make small incremental changes so that you'll know what change caused what effect.
Since you have new-gen, hoses and emissions connections are slightly different. However, do post photos of your original vacuum connections; they may actually be incorrect. Never, ever trust what PO tells you or have done on bike! Verify
everything!!!.
On new-gens, emissions is simpler, so you don't have to do much:
1. leave ALL connections to tank alone. EVAP canister is standalone system and doesn't have anything to do with carbs.
2. disconnect ONLY small vacuum-line from "CA emissions-fitting" going up to PAIR valve on top of head, under tank. Cap off vacuum-ports on both ends.
3. run vacuum-lines according to this diagram, it's
better than new-gen's factory configuration. It gives petcock its own dedicated vacuum-line to ensure maximum-vacuum for reliable operations. Then 2nd vacuum line goes to decel-valve. A vacuum-leak here due to cracked lines or insufficient sealing at ends won't affect bike's operation much (compared to having it on other vacuum-port). So basically just swap vacuum-hoses coming off vacuum-ports on carbs.
Note vacuum-T that you've capped off that used to go up towards PAIR valve.
