This is a common symptom when a couple of things are present.
One is: too-soft springs in the spark advancer (this will make it REAL sensitive to anything else that is wrong).
Another is: the tiny O-rings on the mainjets are too old and have turned to plastic now (thanks in part to ethanol), so they leak fuel past them, unmetered fuel.
One thing that may get you running long enough to figure out if the carbs are the culprit or the spark advancer is: retard the spark timing to almost "T" on both sets of points, by turning the whole points plate CCW a little. Then when it starts it will be retarded in timing, making it less sensitive to the spark advancer portion of this issue. If it still wants to jump up and idle at 3500 RPM (like it sounds) then the mainjet O-rings are likely at fault. Given your dark sparkplugs (or were those from the other carbs?), this seems likely.
The biggest issue we are seeing right now in rebuild kits for these carbs is: too-big O-rings in the non-Honda kits. This prevents the jets and the float valves from being assembled properly, even to the point of breaking parts. They are supposed to be 1.2mm in cross-section, but the kits supply 1.5 or 1.6mm instead, causing the trouble. This is the #1 reason why it seems so hard to rebuild the CB500/550/400fcarbs these days!
The carb 'rebuild' consists of (besides cleaning) replacing the O-rings on the mainjets, float bowl drain screws, and the fuel feed tubes, and sometimes the float bowl O-ring that seals it all up. It's pretty simple, especially for someone with fingers as nimble as yours! It's just hard to get the right O-rings. I have tried before (and may try again) to have a local seal shop import a bag full of these tiny ones: if I can get them, I'll let everyone here know about it.