Corey, before you do any cutting you need to get those areas flat. Either with a table saw, plane, rasp, sandpaper backed with a sanding block, etc. Then you can mark your lines more precisely.

For my build I'm using templates cut from a gallon orange juice jug. It works very well and is better than paper or cardboard for transferring the lines.

I also recommend you view the various videos Midway USA has on YouTube on stock making and inletting. http://www.youtube.com/user/MidwayUS...making+a+stock