I put the windex in a little spray bottle and just pump about 9 - 12 sprays straight down the bore with the magazine assembly and bolt removed (this is a mosin nagant m39). the muzzle rests stright downward in a cardboard box with a bunch of rags in it that i keep in the yard. after about 30 seconds i lift up the m39 and all the windex runs out black and blue.
i shake it dry, then carry it into the house where i invert the cradle (so that the muzzle points down instead of up) and run several more windex patches through follwoed by dry patch. then i use CLP after a few mintues of drying time.
I dont want to use wd40 because i want to use as few chemicals as possible. windex is pretty good old stuff so im not too worried about it. even so i try not to inhale too many fumes, esp with the CLP.
as long as you dont splash stuff everywhere your stock will be fine. that's true whether you use windex, clp, sweets, etc.