You say your bike is a '79 but from the jet sizes you've found in your carbs, it would appear you have a '76-'77 carb set. Now, I've said this probably about a million times before but I guess I need to say it again - you must positively I.D. the year of the carb set you're working with in order to properly re-jet it. Re-jetting is based on what was stock in that year carb set, not the year of the bike.
If you actually do have a '76-'77 carb set, it came with very small mains (those 122.5's), the smallest ever put in a 650. They work fine on a stock bike but are quickly out-paced if you have mods. While many of the other carb sets may be fine with just one or two sizes up on the mains, this set usually needs more. My recommendation would be one up on the pilots, needles leaned a step, and 130 or 132.5 mains.
But, before you do any jet buying, we have to I.D. those carbs. If they are '78-'79 carbs then the sizes I just recommended won't work.
What you will want to buy is new air filters. Get UNI UP4200s or UP4200STs (dual layer). You'll never get it tuned right or as well as it could be using cheapo pods.
The motor racing and hanging around 3K could still be a sync issue or it could be the carbs being so lean (still jetted stock with mods). To investigate the sync issue, back the idle speed screw on the left carb out so it's not touching the cable arm, then start adjusting the sync screw between the carbs in and out. I can't tell you which way to turn it as it could be off either way. Try both and see if either starts bringing the revs down. If it does, you've got a sync issue, if not it could be the too lean issue.