lots of elbow grease and working down the grades of the sandpaper/wet dry paper. i thin i can imagine where your having the problems? just in front of trigger guard and on base of comb where it joins the pistol grip? though i may be wrong but this is where i have my problems.
as long as you are going to be using a dark stain and not a light one you should find that resatining it will cover any blemishes.
but the most important thing to rember would be preperation! pleanty of time in the sanding then the easy part of restaining
if you do a search on here about refinishing stocks theres pleanty of advice to be had by a more people more knoledgeable than i on this matter. can also get a good few words of wisdom here
sanding stocks and so much more
BTW even if you do take a little too much off the but and have overhang on the butt pad.... rember these three little magic words
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ADJUSTABLE BUTT PAD
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amazing the sins of the paper it hides
hope this helps you a little
ROB