I have had trouble getting an even bite with the rusting solutions if going beyond ~320 grit, and I use a tightly controlled damp box. What I do is polish to 400 to be sure I have all of the scratches out and then hit it with 320 again. I even started hitting it in my bead blaster before the first rusting. This totally evens out any differences in the bare metal finish.
When I first started rust bluing I polished several small pieces of metal to different grit finishes and and then rusted them. I never could really see the difference between 320, 400, and 600. Well, except for the fact that the 600 grit piece was spotty, especially in the first few coats. Then when I started bead blasting after final polish, I rusted some small test pieces and could not tell which one was hand polished and which one was hand polished followed by blasting.
I have read in several places where the action of the rust is about equal to a 320 grit finish, so anything from 320 and up will look the same. Don't know how true this is and how this was judged. It oculd be one of those things that just gets repeated in gun books without any proof. i do know that each cycle of forming the oxidation layer on the steel, you are actually pitting the surface. As a mechanical engineer who has spent waaaaay too much time in the lab testing different materials, I have a hard time believing that the pitting action can be fine enough to see the difference in a 400, 600, or 800 grit finish. But I could be all wet here.
Anyway, You can control the finish by controlling the bite of each rust coat. If you let the parts get a very fine rust layer and do more cycles for the finish, then it will look noticeably different than a blue job where you do fewer cycles but let the rust really bite and build up heavier layers each time. THis will have the effect of looking "more polished," but all you are doing is controlling the physical pitting of the metal surface. I can't adequately stress how much you have control over the finished appearance of the blue by controlling the rust cycles. I have had people look at different pieces of my work and comment on how I polished them differently, but all it was is that on pieces I really did not care about I would just do fewer, but heavier, rustings. It comes out more matte and looks rougher. Also looks "blacker" rather than the "bluer" look of finer rustings.
I have said for years that I was going to do a controlled test of pieces of steel with different finishes and then keep then analyze them. I think I will definitely do it this year. Of course, I have said this too for several years, but I mean it this time!!! I am going to force myself to actually do the test in '07.
At any rate, i do beleive that the actual physical rusting of the steel is about 320 grit based on my observations. I know that it is much harder to get the rust to bite on steel that is polished to grits beyond 320. The higher the polish, the harder to get the bite. I am DEFINITELY not an expert in metal finishing by ANY stretch of the imagination, but men whom I respect have told me the same thing.
Just food for thought.
Oh yeah, almost forgot. If you can see pits now, you will see them in the finish. If they bother you, and you hav eenough metal there, then file them out and polish to match the rest of the gun. If it is in a thin spot on the barrels or something, then you may have to live with them.
As for your areas looking differently polished, it has been my experience than as you get to the 5th or 6th rust coat, then eveyrthing will look just like a 320 grit finish that has been risted. If you have any scratches that are more coarse than 320 grit, then they will show up through the blue, just as the pits will show through. As stated above, I blast the metal for an even finish, but truth be told I don't think it matters when going to 6 coats or beyond. But psychologically it helps me not worry as much, so I do it!