Also, try real hard to find another airbox for the 1979-80 CB650. The carbs are EXTREMELY sensitive to incorrect airbox pressures, so much so that Honda made several versions of that airbox to get them to work right at speeds over 40 MPH, because wind turbulence behind the engine (which is entirely normal) was causing the power to flatten out noticeably between 40 and 70 MPH, and changes in side-winds (like when crossing Kansas) could drop speeds by almost 10 MPH when they blew ACROSS you (not AGAINST you). Those carbs were Honda's first "low emissions" carbs, and only lasted 2 years because of the troubles. The airbox is critical if you're riding anywhere but around town.
Jetting: find some OEM jets and use them. The term "rebuilding" as applied to these carbs is downright scary: I just finished spending more than 3 weeks fixing a 1979 CB650 (in otherwise nice condition) that had the carbs "cleaned" by a local "vintage bike shop" in Denver: they had 4 widely different settings on the idle-mix screws, the #4 carb's intake side hose (from the airbox) was open by 2mm along the outside (pretty obvious issue, wouldn't you think?) and the bike sounded like a fireworks display when it was running, which took me a week to make happen at all. The float levels were also at 4 different setting inside the carbs.
...and all they did was 'clean' them?
In the end: set the air screws at 1-5/8 turns out from fully (gently) closed for your starting point. If the O-rings in the idle-mix screws are hard and flattened, and/or the tiny flat washers in there are cupped (from being tightened too tightly, and warped) then your idle-mix settings will have to be a little tighter, at around 1-1/4 turns. If it won't run in these ranges of the idle-mix screws, which are active in these carbs up to 3500 RPM, then check your float levels and also for cracks or holes in the diaphragms on the left side of each carb (easy on #1, not so much on the other 3).
"Rebuilding" these carbs involves, first and foremost, replacing the tiny O-rings in those idle-mix screws, and making sure their washers are smooth and flat. Then their setting is 1-5/8 turns. The float valves must make all float levels the same in the carbs, at 12.5mm (0.50"), and the rubber on their tips must be pliable, or they will not seal. The mainjets must be #90 size, in Keihin brass. A #105 jet is more than 15% richer than normal, so it will blubber, sputter, and blacken sparkplugs quickly, way too rich.
What makes "pod" air filters so bad on these bikes is: when you are rolling down the street the air between your leg(s) and the carb(s) flutters. Each time it flutters it also tries to open those (anti-smog) diaphragms on the sides of the carbs, which makes the mixture drop to lean for a moment - then the engine stumbles. The special airbox(es) that Honda made (and replaced twice on this bike, under warranty circa 1979-81) were designed to stop this outside turbulence from 'popping' that air cutoff diaphragm, which made the bike alternately surge and fall on its face. With "pod" air filters you will have no chance of making the carbs stop that activity, as those make for no differential air pressure between the diaphragms and the air pressure in the throat of the carbs.
...which, IMHO, is why the 1979-1980 CB650 bikes change hands so fast these days...they don't want to run right when these critical parts are stripped off the bikes. So, the owners give up and sell them. You can buy one here in the Denver area for $300, almost any time.
