As I understand it. One risk area on the CB550 engine is with the primary chain, which has no tensioner. It tends to fly outward at RPM and with wear and "stretch", it gets into contact with the engine case. Keeping the carbs well balanced with help with the primary chain wear. But, before I put my 50K miler back into regular service, I'll be checking the primary chain.
I've no experience with the 650 cam, or jetting for it. But, I assert you are just guessing with the jetting. One possibility is, of course, that you are correct. Another is that the WOT range is now too rich and the plugs clean up with a lean mid range throttle position, making the "average" plug read look reasonable.
Probably the only way to know for certain is to have it dyno-ed and a fuel map/chart printed for it. $$$
Of course, you can just run it till it drops and spend that money on parts. Or, if you frequently roll "7s", hit the jackpot!
The old saying goes: "You can tell the pioneers, by the arrows in their backs."
Cheers,