I think sanding a stock to 500 grit is extreme, not less 1000 grit. Of course, you could avoid the whole problem by carefully scraping instead of sanding. You may still get iron filings down in the wood fitting your patchbox. I have gotten the gray iron stain on my guns before during the whiskering process. If you are staining with AQ, I have found that the iron in the stock is a non issue. It will just be turned red and blend with the stain. Rub it down with a white ScotchBrite pad is it is too dark after staining.
I am going to make an editorial comment here that I know I shouldn't but I am going to do it anyway. I can't believe how picky some of the builders are on this board. Have you guys ever looked at the original guns? I have, taken quite a few apart and worked on a few. When it comes to things like the inlets being tight where you could see it, they were very good, but I think a lot of you would be aghast at the work you couldn't see. Lock mortices and barrel channels were just hacked out in order to get the part in there. File work was finished only on the surfaces you could see. The bottoms of the barrels often looked like they had filed them with a rasp. Surfaces were not symmetrical including lock panels. Usually, they lined up when viewed from the top, but not always. They just got it close. Thimbles were not filed exactly the same. Again, they got the design the same but the execution wasn't identical and they did not finish a 1/16" that wasn't seen. Usually, they just cut right through the web when inletting barrel tenons and thimbles because the ramrod was going to cover those things. As to finished surfaces, they just smoothed things out, getting rid of most of the tool marks, but not all. The background of carvings was not flat and smooth. even in the best carving. It was smoothed out using chisels or knives and left a little rippled. Just lighten up some and build these things in the workman like manner they were built. If you do, your guns will look like they came out of an 18th or 19th century shop and not a Japanese auto plant.