I've built from crooked blanks before. I use the top flat of the barrel and the centerline of the length of the barrel to reference everything. It helps to assume that nothing is on the wood is true, and to measure everything from the barrel and trust your measurements. As I build, I like to keep certain key areas symmetrical and square, like the lock flats and forearm, that way I just split the difference to find the centerline on the bottom of the gun.
I also use a string and plumb bob technique to lay out the butt plate. I level the top barrel flat sideways in a vice, mark two center marks on the barrel at the muzzle and breech, stretch a string down the center of the barrel past the butt, then hang another weighted string so that it nearly touches the butt of the stock. This will give you the centerline of the buttstock and the vertical line for the buttplate. From this center reference, you can add castoff and cock the buttplate if you want. (Thanks Fred, I learned the tilted buttplate thing from you). Bill