He changes out the diodes and some of the capacitors with higher quality ones. This usually does add more clarity, a slight more low end, and generally makes the pedal sound sound more like natural amp distortion. But honestly the sound is not that different, I owned the keeley ultra mod and the analogman modded ds-1 for a while and then a regular DS-1. None of them sounded all that different, in the end I didn't think it justified the expense and sold all three and bought a germanium fuzz pedal.
For the price of the modded pedal there are a lot nicer pedals out there. You're better off buying a high end boutique distortion that's going to sound a lot better to begin with.
