I've been thinking about this, and I keep ending up with a Telecaster very similar to the Baja I already own.
It's not the extra pickup/s switch options, to be honest I rarely use those, I think it's the soft V profile neck that makes it so comfortable for me to play.
So I suppose I'd go for a soft V profile neck Tele with upgraded pickups, maybe Texas Specials, and top of the range hardware.
Probably a natural finish with absolutely no relicing.
Considering all the possibilities of an imaginary custom build I'm a bit disappointed in how run of the mill my 'ideal' guitar actually is.