Been through this many times. You either have clogged idle jets, an intake air leak, or a high exhaust leak (not likely, but it can happen.) Most likely, given the cleaning you've done, it's the idle jets. Especially, since the idle screws were still plugged, the PO put on the K&Ns and then it wouldn't idle. That's when he parked it. Since you've already put the stock breather back on, it's almost certain that it's the idle jets. If you have the carbs off, pull the bowls and slides, then hold the carbs up to light. You should see pinholes of light through all the jets. I bet you don't. The jets may be down in the tubes and you'll have to get a skinny screwdriver to get them out. You might be able to unplug them with a welder's tip cleaner without removing them. Seafoam and the like won't work if they're completely clogged, because if the fuel can't get through the circuit, it can't dissolve the crap. If you can get them out, soak them in Berryman's B-12, that you can get at WalMart. (Army Chopper mechs use it--- stronger than Seafoam--- careful, it'll peel paint!) If not, use the welding tip cleaner or a strand of wire from a wire brush to (gently) unplug the idle jets. The jets are brass, so be careful if you use the wire method, 'cause if you wallow the holes, they're shot and need to be replaced. Once you can see through the jets, you can put the carbs back on and it'll start and likely idle. You can get the sync in the ballpark by looking at the slides as you work the linkage--- they should all have the same size opening as the slide goes up and down. By the way, check the diaphragms on top of the slides while you have them off. Stretch the rubber and look for pinhole tears, especially around where they're bonded to the metal. Sometimes you can fix them with liquid tape. Replacing them is better.
You can put the Berryman's in your first tank--- use about 3-4 oz. It'll run a little rough until you fill up again. Just don't get any on your paint. Once they're clean, you may not even have to touch the idle screws, especially if you're going to run the stock airbox. If you kept the original settings, you won't have to do much adjusting--- Honda does it right, and I always recommend cleaning the linkage with WD-40 or something on any old Honda that runs before you touch any of the adjustments on the cables or anything. Only adjust or repair after you've rode it a couple of hundred miles, because some things are just stuck and will work loose by themselves.
Sorry this is a bit long winded. And if you've already done this stuff, disregard!!!
"I don't practice what I preach, 'cause I'm not the kind of man I'm preachin' to."