If the glue spot doesn't come out with sanding, be ruthless, get some really coarse grade sandpaper and really give that area a work over, then use some appropriate coloured wood filler to get the area flat with everywhere else....any staining should impregnate the filler, leaving you with a even looking finish to the rest of your guitar....try getting rid of the glue first though.

With the dyes, are you using powdered ones or premixed ones in a bottle?