well there are several techniques.. first of all I stay away from water based anything. they just don't work like the oils do. there are gel stains, stain pens, colored pencils designed for such things. I've even matched wood colors in paint and faux painted areas and you couldn't tell. I have many years experience as a professional painter though. what color stain did you choose? also have you tried multiple coats? how old is the stock. a lot of new wood is coming out so green that is repels stain. My bro had an old 22 mag that hadn't been taken out of the case for 15 years. the wood had shrunken so much the trigger gaurd was loose and the action screw looked like it had backed out. also your finish can be tinted with oil based stain and after several coats of a stain/oil mix absorbing into the stock the areas tend to be less noticeable and appear more as "character" in the wood. can you give more details, or possibly pics