When you jet carbs on a a motor, four things affect it - comp. ratio , ignition advance, the exhaust system and the fuel you are using. If the comp. ratio is high usually requires bigger jets. If the ignition advance changes it can have the same effect as changing the jets in the carbs. I would set the ignition advance to the specified value for the commando engine for the fuel you are using. Fit a main jet which is miles too big. Fit the normal sized needle jet and needle with the clip in the middle groove, and a number 3 slide, and start the bike. As you wind the throttle on, if it gasps you know the needle jet is either too small or you need to lift the needle and change the clip to the bottom groove. If the motor still gasps, you need a bigger needle jet. Getting the needle and needle jet right is critical. You should try to get the situation where lowering the needles one notch causes a cough as you change gears when riding the bike - then raise the needles one notch. The last thing to try to get right is the main jet, that takes high speed runs and plug chops.
The needles come in various tapers and getting the right taper is important if you are trying to get the most performance. Two things interact - the shape of the taper on the needle and the ignition advance curve.
Don't ride the bike for a large distance if it is jetted lean. If you take a muffler off your bike and fit a megaphone without re-jetting, you will probably burn a piston if you ride the bike any distance.
Hope this helps.
Best Regards,
Al