TPI, you must have done something wrong, but it's unfair to blame Common Motors for it. Over the years I have glanced at a wide variety of sites which demonstrate maintenance and I have seen a lot of nonsense and/or inaccuracies. Although I myself would not do everything exactly the way they do it, I find Common Motors vids quite good. They prefer to keep it simple and above all, their presentations lack the hysteria that characterise others and is so hard to endure by Europeans. As a matter of fact, if I was forced to recommend just one site, it would be theirs. I'm aware it's a commercial enterprise, but in general they inform real well and they certainly do not deserve the bashing you gave them.
I don't know if you've only worked on the carbs or also did other maintenance at the same time. Anyway some remarks.
Many, also in this forum, misunderstand the role the #38 (CB550) and the #40 (CB500) jets play in combination with the airscrews in the whole functioning of these particular carbs. In the UK site, K2-K6, not that long ago, has shed a good light on the subject, but I cannot find it right now. I will try to find it.
These jets are often referred to as 'idle' jets and that's where the misunderstanding begins. AFAIK Honda never called them idle jets, but slow jets. Important to know, is that, contrary to popular believe, these jets, together with the airscews do play a role also in higher rpms. If not, you would have needed larger main jets. In the 80s a Honda mec, who owned a CB500 himself, had already instructed me on that.
Out of curiosity I have played with various settings of the airscrews, but I always returned to the one turn out, Honda advised and I cannot for the world understand how CB500s in the US can perform well with the two turns out, a US service booklet suggests. IMO the data in forsaid booklet has its origin in an error Honda has made on p.165 in the Shop Manual Honda CB500-550.
When the slow jets are interpreted as idle jets, many make the mistake trying to arrive at an highest possible rpm @ idle by turning the airscrews out. It's very tempting as your engine will purr like a kitten, but as TT has already suggested, acceleration will be out the window.
I'm pretty familiar with various ways of syncing and I can tell you from experience that you shouldn't expect to do it a 100% right, the first time you do it. You have to build some experience. Increments made should be minor, there's waiting, settling, listening, a bit of revving, etc. Also all adjustments should be within the limits, Honda has outlined in the Shop Manual. The cutaway also plays a role. In the past I may not have expressed myself well. It's not so much you need a filthy rich idle in it self, as well as that the slides must have a wider opening than you would have by trying to arrive at an highest idle rpm by turning the airscrews out. Another mistake many make, is interpret a scheme on the carbs working fields, also often presented here, as too litterally. Realise that all systems work together and there are overlaps, wider than you'd maybe think. This overlap is often the first, people forget when seeing such a nice clean scheme. When you realise there's cruising and accelerating, you will also understand these carbs are simple compromises at best. From experience (including experiments) I know the scheme below represents best how my CB500 carbs work and I assume your CB550 carbs will not much differ. I find it sad that you, like so many others, have chosen to change the position of the needles. IMO that's rarely needed. Most can be done with the slow and main jets and the airscrews, that is on our carbs which lack acceleration jets.