I've got something of a custom guitar myself (Although I've done a lot of custom work on all my guitars). I took one of my prized HM Strat necks (its wider than normal strat necks, with a flat fretboard radius, so its much like an alan holdsworth guitar). Stuck it on a custom made semi-hollow strat body made by a friend of mine..and well thats about it. Jumbo frets but all the frets are slightly scalloped out (getting deeper towards the 24th). Its got both the Dimarzio S3 that came standard with HM Strats, and a piezo system I bought off the Carvin custom shop (I practically had to lie, said I had one of their custom guitars). The thing is routed for two outputs (like a carvin), so I can have the acoustic sound or electric whenever I want. In the neck position is a dimarzio paf pro.
Of course it looks like crap because theres no finish on it yet ;( And its all in pieces still.