Go for it!
The symptoms you describe are common, and usually easy to fix. Needing constant choke (to run/idle/pull hard) points to plugged pilot jets, and a removal and thorough cleaning of all brass jets is indicated.
If the bike ever ran well with the current intake filter setup, then it should run well again. If you can't verify if it ever ran well with the current setup, going back to stock before assuming that it will run well is a good idea.
All the best,
Shane
Looking at the Haynes manual I don't see pilot jets in the schematic, but only Pilot Adjuster Screw. Would that part of the carburetor be under another name?
Perhaps "intermediate jets" or "slow jets", they go by several different names, are usually right next to the main jets, smaller, and depending on exact type, may have a small emulsion tube as part of the jet itself.... but now that I'm looking at the schematic, yours are a bit different...
Looking at the schematic of your carburetors, and they do indeed have some differences, like an accelerator pump and air cutoff valve. There is also a "screw set A" that's part of the assembly. Here's the link:
http://www.cmsnl.com/honda-cb650-1979-usa_model472/partslist/E++1801.html#resultsYour carburetors are more complex than some, but not really too bad. In addition to removing all the float bowl components and making sure that carburetor cleaner shoots through the various passages, I would take the accelerator pump(s) apart to ensure that they are not crusted up inside.
Also, part number 19 in the diagram is the "holder, needle jet". Get this thing out of there and make sure that the little tiny holes along it's sides are clear. There should be about a dozen holes in this tube--they need to be clear, and sometimes don't come out with the main jet.
All the best,
Shane
