Then when I got the message through my contact form asking me about the Vpp Voltage Error I decided to pull mine out and do some debugging again. Only this time I compared it to a working unit. I probed the various points of the working programmer with a probe from my oscilloscope and saw that the Vpp voltage on both sides of the L1 inductor were 5 volts at idle.
I remembered seeing a lower voltage on one side of the inductor in previous tests of the failed unit so I probed it again and found that the L1 inductor had 5 volts on only one side. So even though I had replaced it, it was not working as expected. I disconnected everything connected to the dead side and still the voltage was zero. This told me nothing was shorting the inductor to ground as I thought may have been happening. Could I have replaced an inductor with a bad inductor and created a new problem in addition to the wrong resistors?
I removed the old one and then carefully bent the leads of a new inductor to fit the hole spacing in the board but with a relief bend in the lead instead of 90 degrees. This left the inductor sitting off the board but at least the leads weren't bent 90 degrees.
So take this as a lesson if you build the PK2 design, make sure the inductor is not bent too tight to break the inner wire. Apparently some of them are very fragile. I will fix the layout in the future so this problem doesn't happen again. I sent the reader an email describing this but have yet to hear if it was their problem as well. I decided to share this with everybody in case anybody else has one of these sitting around with a Vpp Voltage Error.