Hi Mark: This is a great project and a fine use of these parts. I would not worry about the beauty spot. If it is soft, wait til it is stained and then flood it with CA. that will harden or plasticize the spot, and after finishing, will likely disappear.
I'm anxious to see how you proceed with the stock architecture" From these images, it appears to me that about 1/8" will have to come off the comb at the wrist end to make the heel to comb line flat: as it is now it appears that the forward part of the butt plate extension is sunken below the plane of the comb. I know you are a long way from finished, so the following is likely redundant. Presuming the trigger plate is in the centre of the stock, some wood needs to be removed from the off side to even things out. Also, the lock panel could use some sculpturing, beginning with the lock plate forward of the snail. I suspect that these observations are superfluous, but thought I'd mention them now anyway.