It's a funny thing that until very recently I've not understood what Honda have written in their manuals about this subject.
I've read it through quite a few times and we were discussing it recently in a question Julie posted about setting up on a 400, but still I didn't realise what they've said and just how far reaching the routine is.
I agree with what hairygit has already stated, the syncing is for matching the carb slide height and not the tickover. I've always felt that for a lot of situations this is a bit of workshop theatre. OK, I know it's one way of getting the throttles equal without taking the bike apart and bench syncing them, that's fine. Bryanj has always referenced completing all other setup work prior to this and I couldn't agree more, you are wasting your time otherwise with the potential to put more error onto the syncing if another issue is present.
Think it's Hondaman who says that this should agree at 3 to 5000rpm as well to get a real running representation. He seems to know his onions as well as alot of other people's onions as well.

It's common, as on this post, to set the idle jets all to a specific matching turn spec to get the idle more or less ok but the instructions don't say that.
That Honda manual text is so disarmingly simple but it covers off so many escape routes to get the job done.
It calls for you to start with no2 carb idle jet and open it out until you reach the highest rpm with throttles closed. Then turn the screw in until you get a 100rpm drop, then leave it. Readjust the main carb tickover set to correct the final revs to 1000rpm +/- 100. Then move to the other three carbs and do the same for each one instead no particular order. This definitely allows for an individual setting for each carb body.
So, why do I think it's so good?
Firstly if you try adjusting each one, then you'll see if you get a response or not. This would tell you if one is blocked.
Secondly, each one by going to the fastest idle will account for any differences within that carburettor (idle circuit or throttle slide variance) or cylinder as it's using the best burn characteristic to pinpoint it. So you'll end up with parity of the idle circuits and cylinder to cylinder mixture match. Clever ha?
Thirdly, it forces you to bring the throttle slides down until it runs properly on its idle circuits with the attendant fine adjustment and fuel metering that allows (the idle circuit is really a tiny carburettor) and this is why you shouldn't do carb vac syncing at tickover ( the mains don't meter properly and the fine adjust of the slides is nowhere near as accurately resolved as idle circuit tapering) with the handover from one to another jet range taking place only when the throttle are partially open. Makes sense Hu? I thought that was very neat.
It's more or less what current engine strategy is doing via ecu nowadays, but the Honda method is by necessity open loop with no feedback, it uses you as the loop closer in place of sensors and fast processing to. But it is the same thing contained within a different time frame.
If anyone has read "Zen and the art of motorcycle maintenance " how to adjust the idle screws on a motorcycle is central to the core argument placed of do you train people to theoretically pass an exam or practically to actually be able to do the job, really do the job in question.