I have been doing some experimenting with staining using a water based dye stain from General Finishes.* It's been reasonably good, but only comes in very limited colors. It worked best over untreated wood. Not so well over sealed wood. It was very blotchy over wood that had only been treated with AquaCoat clear grain filler. Although I don't have a lot of experience, I gather that is not an unusual experience trying to dye stain over wood that has been sealed.

While looking for a harder water based finish than the one I've been using I ran across CraftNique gel stains from Crystalac. They advertised that CraftNique could be put over finished surfaces. I decided to see how it would work on my blotchy piece... Here's a pic of the piece with 1, 2 and 3 coats of dye stain over AquaCoat grain filler.

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I put added two coats of CraftNique gel stain on top of the the piece just to see what would happen.

Click image for larger version. 

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Much nicer. Works very well over finished pieces as well after a light, scuff sanding. Since I have a bit of a propensity for sand-throughs, that feature may be important ;-)

If you get the full CraftNique color system it's very pricy, but the individual pre-mixed colors are not too bad. I have also found that if I can darken the color a little by adding a drop or two of acrylic craft paint, although I am guessing the mfg would not approve...

*More on the experiments here: https://www.buildyourownguitar.com.a...t=10529&page=4