Please, DO NOT ruin that nice wood by trying to color it with some rainbow choice!!!! If you want, sell me the walnut and mahogany and I'll hook you up with some alder or basswood to ruin!!!!
Walnut is a beautiful wood, and you will almost never see it with anything other than a natural finish. I would maybe say to use a dark walnut zar stain if you insist....... Maybe at the most a little black grain filler in the mahogany and the walnut, but please, please don't ruin that wood with some sort of dye!
Glad to hear there is someone that is scratch building their own guitar!!!!! One suggestion I have is to buy a good neck rout template!!! And a great router. Spend as much money as you can possibly afford on a router, buy the best machine that a real tool dealer sells!!!! (Not Lowes or Home Depot, they only sell junk japanese tools) And also, spend some money on your cutting tools, drill bits, router bits, saw blades...... Hard wood is just that, hard. It is hard on tools and with walnut as Cagey said, it creates a really fine dust that makes you sneeze like a mother phucker! And I almost forgot about the brown walnut snot you will have in your nose for a day and a half!!!!
One more suggestion for you is to make at least two body blanks, one to do fitment and work out any problems and one to perfect what you learned on the first one. You will make mistakes and learn from them....... Like forgetting to drill a hole after you finished the guitar etc..... And if you don't chew up your prototype too bad, you will have two guitars when you are done!!