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Nick, I haven't had any trouble with the stocks that I strip. I make sure to let them dry for about a week before to make sure any moisture is out. I hang mine close to the ceiling to dry, but a drying box is handy if you have one. If you let the water soak on the stock, of course it will enter the wood. I wash mine with lacquer thinner and then use a wash cloth with clean water and a heat gun to raise the grain before finish sanding the stocks.
The stripping process saves me more than a few hours of labor and the results have been just as good as what I used to turn out when scraping and sanding the finish off.