Permalyn sealer is shiny as applied. So is the Permalyn finish. They're both the same product, the sealer is just thinned.
I wouldn't rub it back yet. Use a small cloth liberally soaked with sealer and apply to the stock by gently wiping. Should take all of a couple minutes to do the whole stock. Let it dry a few to several hours until it is no longer tacky, and feels dry. I'd apply a couple more coats in this manner, then let it sit for around 24 hours, so it's good and dry.
To knock the shine out do the following. Get an old tooth brush (or new), medium stiffness, and scrub the entire stock with a slurry of mineral oil (or paraffin oil) and #4 pumice stone. I use the tooth brush to slather on the oil, then shake a small amount of pumice stone onto the oil. Scrub with the tooth brush in an area, then wipe off with a rag. Be careful not to scrub too vigorously or you'll go through the Permalyn. After some trial, you'll guickly see the desired finish. I personally prefer this scrubbing method to using scotch brite pads because it's less aggressive, and is especially good for getting into carving, if you have any. It will leave a finish that appears very warm, and not excessively shiny.
Ed