> My biggest issue with DIY boards is drilling the holes and in particular getting the bit in the center of the pad. This is such a pain, I now just use pre-drilled protoboards and hookup wire on one-off or prototypes.

I haven't done it with PCB, but for wood when I need a precise location and have no drill press, I use a nail to make an indentation and use my smallest drill bit to drill it through, then I can use progressively larger bits, as they will tend to self-center in the hole.