Well here is what I have found. Korg gave me half the story via email, I then figured out the other half myself. This has reset all of the MIDI CC, which is about all I changed, so your mileage may vary.
1. Press 1 and 2 and Sampling while powering on
the KP3.
2. PrLD will appear in the LED.
3. C will be on, D will be flashing.
(This is where Korg left me, after waiting and not seeing any change I pressed D. I know, genius!)
4. Press D.
5. urt will flash in the LED.
6. P.off will then appear in the LED.
7. Power off and on the KP3, enjoy factory reset goodness.
HTH,
-JR Miller