Marring the outside of the pilot jets is no big deal.
The big idle knob is set for idle when the engine is at operating temperature.
The choke has a separate fast idle cam that increases idle with choke application, and it has its own adjustment screw to set rpm when choke is needed. It will need *some* choke until it warms up, if the carbs are clean and adjusted correctly.
The idle mixture screw is NOT used to vacuum balance carbs. The balance adjusters are under the top caps (#1, #3, & #4), as described in the Honda shop manual.
The idle mixture screw settings are in the manual too, but the settings won't be relevant unless you also have the stock air filter and exhaust system. (I didn't see a description of those for your bike.)
If the pilot jets were gummed up, I'd expect the accelerator pump system to be gummed up too, which would affect the throttle twist response.