This question can be divided into two main aspects, visual and practical.
On the esthetical side of things, you may already know exactly what your dream guitar will look like, you may want to make a replica of your favorite guitarist or the one that changed your life. In that case it will all be a little easier to figure out as it already exists and you just need to find the right specs and measurement. (Read on, they may actually be here). Where it gets tricky in when you either want to customize ‘just a little bit’ or go all in and create a completely original design.
On the practical side you may already have a concept of what type of neck, scale or pickups you want, what type of sound you are aiming for and the type of guitar that feels best to play. Eddie Van Halen created his famous ‘Franken Strat’ because he likes the Stratocaster, but wanted to upgrade it to his own need. Steve Vai took it a step further and designed a guitar from the ground up according to his desire and together with Ibanez created the ‘Superstrat’. You can mix and match parts, styles a specs to create or experiment with whatever you like.
Body and Neck Material
The material the guitar is made of makes a big difference to how the guitar looks, feel and sounds. Without getting into exotic materials the question is usually around what type of wood to use. (much more info in ‘Guitar Wood Types – Explained’)
The most commonly used woods are Mahogany, Maple, Ash, Alder, Basswood, and Poplar, with Darker types such as Rosewood and Ebony used for fingerboards. With your own build there are no hard and fast rules although it is advised to steer clear of softer timber such as pine and very hard ones like Oak or the Brazilian Ipea. The latter are just so hard, it’s a pain to work with. There are environmental concerns as well and some types of wood are getting harder to find with alternatives becoming more common.
Specs!
So, you figured out what you want the guitar to look like. Now find the specs that match your passion, your whims, your budget and the skill of whoever is going to play it. If you’ve ever looked at all the specs of any guitar, you may have been blown away by the amount of details. But all these details are exactly the ones you are going to have to figure out and decide on. Scale length, number of frets, type of frets, neck thickness, neck shape, fretboard radius, pickups, strings, electronics and lots more.
Some of the specs have to do with comfort and are totally subjective, and other will have more to do with the sound of the guitar. Without getting into ‘tone-wood’ and its effects the two factors that will affect the sound of your guitar most are (arguably) the guitar scale length and the pickups.