This was the very first circuit I built. A great learning experience. Here's what I found:
NONE of the values are super-critical for getting it to sound 99% like the clips on the Zvex site. I've never had one in my hands, so I can't say for sure, but mine has Si trannies, wrong resistor values, etc... and it sounds just like the ones in the videos. Why you may ask? My hunch is that the 5 controls allow you to compensate for differences in components.
For the PNP and negative ground "problem," see here:
http://www.muzique.com/lab/reverse.htm and here:
http://www.muzique.com/lab/fuzzface.htm ...problem solved!
It can work with the battery connection reversed, but it's quiet (oops)!
Paperhouse, your problem *may* be that your signal is just too loud going in... Instead of a series resistor, wire a guitar volume pot (voltage divider) at the very front of the circuit. You can then dial in just the right amount of roll-off without worrying about the controls on your guitar.