In addition to the wood species you will use in guitar construction, there are other hardwood species you should have on hand to aide in assembly.
Use the cherry for jig making. No wood cuts, works, bends and machines as a nicely as cherry. You will use this all over the place. We work in a custom cabinet shop and so are blessed with a ton of the stuff. Order a plank or two from Woodcraft.
Hard or rock maple is great for jigs where super strength is needed. It works like iron and is almost as strong. A 1.5 x 1.5 x 18 inch block is super handy. Smaller blocks are also handy. We made our bridge caul out of this wood.
Soft pine is great for clamping blocks. You never use this as part of a guitar, but it is great clamping blocks. Softness reduces the possibility of denting guitar surfaces when clamping.