It can be as easy or as difficult as you wanna make it. You can buy pickups on ebay that are already soldered to pots so all you'd have to do is wire it up to the output jack, you can get neck's that already have the machine heads fitted so no drilling needed there. just make sure you know your measurements. if you're looking to make a strat style guitar, the neck has to fit in the neck pocket as tightly as possible or else the strings aren't gonna line up porperly and could come off the fretboard when you're playing. it also affects how well the guitar resonates.

If you're not after anything special then i'd try and get everything from ebay,because warmoth can get expensive. if you can't find anything on ebay that you need then look at www.axesrus.co.uk or www.highlystrung.co.uk these have loads of parts, especially axesrus, they have everything from pickguard screws upto mid boost circuits and they do free postage.