UPDATE 12/13/15
Apologies for the many typo's in the previous post. Posting from the mobile browser was a bad idea.
I will be conditioning the leather, my current plan is mink oil. Any other ideas?
After the suggestion to try acetone in place of the rubbing alcohol I was able to get a much more even stripping, on both shoes. The one had only the original dye and was able to get the last stubborn spots and blend in the remnants. On the shoe with the new dye, the acetone quickly removed enough of the new dye to even out the old dye underneath. Both shoes accepted the new dye very well, and I was able to get even, matching colors between the two shoes.
I have noticed the leather is not as supple as I would like it to be. I plan on liberally applying mink oil. I am assuming the mink oil will waterproof the leather. But will it seal the dye?
If I plan on burnishing, at what point would I do this.