Set your base idle when the engine is hot, then check/adjust your ignition timing. Kill the engine and let it cool off completely. Start your engine, then adjust your fast idle screw on the throttle linkage so it's at the recommended cold idle rpm. Let it warm up and see what it does, take it for a drive etc. The secondary throttle will not open unless the primary is almost fully opened - it acts as a lock out as the Mikuni is a vacuum only secondary carb (this is an emissions thing on Mikuni carbs...) This carb is a biatch to work on but if you follow adjustments in order, you won't accidentally introduce a running fault (e.g. trying to adjust your idle speed by using ignition advance instead of setting the throttle stop and idle speed adjustment screws first) Good luck. It's an art working on Mikunis but once you decipher it's dark magic, you can get back to driving this thing lol.

*if you beat it and it passes emissions, you can reset the engine tune and get some hidden power out if it (just remember to adjust it back next time it's going in for smog)