Ok, a few things going on here.
1. When etching in FC, the etchant will exaggerate the grit marks, because in effect, it is eroding them further. So, the lower the grit, the more pronoun the lines will be AFTER etch. On Damascus and stonewashed blades, I always go up to at least 1,000 grit, but most often 1,500-2,000.
2. The darker areas of etch is likely happening because the hardness of the underlying steel is different than the lighter portions. This, in some cases, can be indicative of the blade having a unfavorable heat treat/temper, or because you knocked the heat treat out when grinding by getting it too hot. If you got it a straw color, I imagine you're fine.
2a. Now, how to fix the dark spot. When etching, you are eating away steel and forming oxides. When there are variations in the hardness of steel, finish, or light contaminants. There is a process you can follow to minimize this effect while etching. It can be a temporary effect in the final product, if you'll do a little work for it.
2b. When finishing your blade and preparing it for etch, you'll want to take it to the final grit, in my recommendation, as high as 2k, and after, you'll want to clean it with acetone, and wash it with water to make sure any particles and oils are off of it. You can switch up order of operation of water first and then acetone in order to test how it works for you, but I want oils off first, and then to rinse everything, so that works for me. Once you do that, don't touch the blade with your hands, or sit it on anything dirty. Right into the etch it should go.
The cycling for FC is entirely dependent on the reaction of the steel to the etchant. There is, however, one caveat. The more oxides that build up, the longer the etch will take, until the oxides create a resist. If you leave a piece of highly resistant steel in a bath for 30 minutes, changes are the oxides are building up, and slowing the reaction of your etch. The time you have it in will have diminishing returns the longer it goes, if it's building an oxide layer. This, of course, is not solved by leaving it in overnight. You'll find an undesirable finish on your blade if you have deep scratches and allow it to eat away for long periods of time.
I focus on sprints. 5-15 minute cycles, anticipate 4-6 cycles, or until the desired finish is there. There is no magic, there is only patience and constant evaluation. In between cycles, I will use sandpaper and lightly sand the oxides off, starting with the next grit up from your finishing grit. So, if you got it to 1k, hit it lightly with a 1.5k. This goes on up the grits to 2.5k-3k. Very lightly. You are not looking to remove all of it, just even the oxide layer and expose lightly etched or non-contacted steel. In between cycles, the blade is Windexed or dipping in a baking soda bath to neutralize the etchant, and to allow you to run it under water and sandpaper it. Then back into the bath. Do this as many times as it takes to get your desired finish. Keep your cycles time as low or high as it needs to be for you to remove enough oxides to even it out, and cycle as many times as you need to to get the finish you want.
Think of it as building up layers. But also think of it as those layers working against you if they get too thick in some areas. You remove some of the material in order to expose the areas that haven't received as much corrosion.
I hope this helps. I provided two examples of my etched blades to show you what outcomes I get. One is a stonewashed finish after etch, and the other a standard etch w/ an instant coffee etch of 8 hours after. The coffee etch works really well to provide a deep black color, but the corrosion will minimal on stainless. I have it pretty well dialed in. The thing to remember with your etching process is that the fundamentals are the same regardless of high carbon or stainless, but the stainless will have a slower reaction time and require more cycles, because the metal composition is designed to reduce corrosion.
