When I got the bike which had sat for several years, I cleaned the tank to squeaky using vinegar and a length of chain(followed by baking soda rinse, water rinse, rubbing alcohol rinse to speed water removal and drying, and finally a rinse with gas/motor oil to give a little oil coat to guard against flash rust. Then I drained and flushed the carb bowls (nasty green stuff came out) and changed the fuel filter, all before I attempted a first start. We got it running and rode to my experienced mechanic, who removed and cleaned the carbs, set timing, cleaned and gapped the plugs, set valves, then tuned and synced the carbs (as best he could). Of course the carb cleaning doesn't rule out some tiny bit clogging a jet or something since then.
We've been riding it since then, dealing with the bogging issue. I haven't looked at the plugs myself but will check them and get pics when I can.
Question: If the aftermarket muffler is causing it to run rich, I can drill it out to open it up a little bit. Any thoughts on this, or do you think this might be the case.