It seems you're just after aesthetics, but I would like to discuss a few things you bring up.
Let's clarify a few things:
Typically a honesuki is ground NOTHING like a yanagi....not even close. You sharpen them nothing alike and you should draw no comparisons between the two when sharpening.
Typically a honesuki is ground something like 80/20 or 70/30....biased strongly towards a right hand user. It is still a double bevel knife, thus nothing like a yanagi which is a single bevel knife with a hollow ground back.
There is no "shinogi" line on a typical honesuki....again, this is reserved for a single bevel knife which a honesuki is not typically.
That said, notice I said typically. It's not always true. In the case of the Artifex honesuki, CKTG's says it's ground 80/20 so I'll use that as I've never seen one. This knife is what I would consider "typical" based on the information I know of the knife.
Essentially what you've done is tried to flatten the large bevel on the right side. This is exceedingly difficult with stones. Stone's dish, wear, etc. and are extremely difficult to get a smooth polished surface across such a large bevel. In fact, I don't ever try to do this as I've done it once and I'll NEVER do it again.
If you didn't overgrind an area, this knife is sharp, and all you're after is aesthetics, I suggest you invest in some ScotchBrite pads....get the coarse and fine....and try to polish the bevel to your liking. This is going to take a while....grab some beers and a few Advil.
If you want, send the knife here and I'll run the bevel across the ScotchBrite belt(s) and try to polish it back out for you for the cost of shipping the knife back. I CANNOT guarantee I will make it look factory, but I can do my best. And it will make the knife dull most likely.
At some point, you would need to thin the honesuki and thus "mess" up the bevel anyhow.....it's the nature of the beast if you want the most performance from your knives.
Another thing, this knife should have a small sharpened bevel on the back and one on the front. This is how I believe the knife came and this is how the knife should be kept unless you're trying for a thinner edge or thicker edge or something else. If you liked the performance from the box, it should look like it did from the factory. The entire beveled should only be ground to thin the knife.
Starting to ramble....I'll shut up now.