Well, I have a copy of the Honda CB/CJ250 CB/CL/CJ360 shop manual and it, too, specifies pilot 35, primary main 68 and secondary main 68. But, I'm thinking that's a misprint right from Mother Honda.
Comparing the jetting to the specs in the Honda CB350 Factory Service Manual, the 350 was jetted with 78 primary and 105 secondary mains.
You asked about which is which, primary and secondary, but you must've corrected your photo, but it is labeled correctly.
Float level definitely can effect lean/rich running, but I would set the float level correct, and go with leaner secondary main jets, if I were you.
Maybe not as lean as 68, but definitely leaner than 100s, because clearly, you're running rich.
In my opinion, those 100 secondary mains you've got are NOT the OEM Keihin jets. They don't have the stylized 'K' that the others do.
How about your air filters? Clogged air filters will give a rich running condition as well. And it doesn't take much to clog the paper elements. In fact, getting them moisture-contaminated can do it, too.
Kirk