I think your idea of doing a neck through is great and I wish you luck on you first build from scratch. It's a little scary but if you take you time and don't rush it you will reap the benifit of your first custom from scratch guitar. Which is something you can be proud of. Doing a neck through is great and i also love the look of the laminated neck. this is where you are in control of the look of your guitar, because there are endless choices of wood you can use. The strength of a laminated neck is much greater than if it was just a solid piece of wood. A much more stable neck it will be.
I am curently building two neck through guitars. One has curly maple with purple heart stripes, and the other has and in this order { curly mpl. 3/4", rosewood 1/16", cherry 1/8",rosewood 1/16," curly mpl. 1/2", rosewood 1/16", cherry 1/8",rosewood 1/16,curly mpl.3/4" .} . It took some time to glue up but it was worth all the trouble it looks awsome. And if i knew how to post picks in this thread I could show you. If you send me your e-mail I will send you some pics if you like. I guess the key to any build is planning and preporation really think through all of the step you need to do to get to the goal you have set for yourself. You can do it and everyone here is in your corner so good luck..