if you have spare parts, you can definitely put together a guitar. however, do keep in mind that there are electronic components to be installed, this, at best, requires some expertise. also, the cost of assembling your own guitar may exceed a shelved, finished, product...
its not an easy task if u dont have pre-made parts.
i've got friends who buy necks with a blank headstock. awesome stuff really to customize it but lots of hardwork as well...
as for just puting pre-made parts together, its quite an easy task. the most difficult would probably just be setting it up. just contact warmoth or usacg, they custom make necks and bodies. but do expect to pay a hefty price
i hate it, i obviously cant build guitar, i should be kept away frm 1. I have these pre-made parts, so basically i just need to drill holes for bridge and neck, i drilled the 6 bridge holes at a slanted position which kinda sucked argh
even premade parts would require quite an amount of measurements, effort and time. unless you get top-quality wood, electronics etc. i'd rather go for an off the rack model as they may be cheaper, and i'm really lazy.