Check to see that your advancer is moving freely. I feel like a lot of folks lately have benefited from giving the ole clean-n-lube job to their mechanical advancers, especially if they've never been off the bike in ~40 years.
If everything else (timing, chain tension, valves) are adjusted properly and you have good compression, then something is definitely up with your carbs. A vacuum leak, they're wildly out of sync, terrible A/F mix, or all of the above. I'm familiar with the CB650's CV carbs, but not the PD variety so i can't give more detailed opinions. The approach I'd take is to read through the FSM and see if you followed the rebuild / assembly instructions to a T.