matt, I didn't stain that guitar. I sprayed it with transparent purple. I wanted the nuances of the swamp ash to stand out, but I could have just as easily sprayed it with solid purple. Make sure that the color coat is very thin, so the grain doesn't get clogged up. Then I mix some pigment, in this case white, with epoxy, and thin the epoxy with lacquer thinner. I spread the filler across the grain and scrape the excess off while it's still wet. Use a rubber squeegee for this so you don't scratch the sprayed finish. Wait for the epoxy to tack up then wipe it down with a rag that's been moistened with lacquer thinner. Reapply the filler and remove excess with a moistened rag as needed. It took me about 3 passes to get it completely filled and colored.
I found that because the finish must be left thin enough to leave the grain mostly unfilled, that sanding the epoxy invariably leads to sanding through the finish, which means you need to sand everything off and start from scratch.
EDIT: Something just crossed my mind. Be careful with the step where you wipe off the excess grainfiller. I used lacquer thinner which is fine for me since I spray an automotive grade finish which, when dry, can not be melted by lacquer thinner. However, I've not tried this method with other finishes. I'm sure many finishes could be destroyed during this step.