Sorry for leaving you hanging guys. I've been a bit busy making preparations for professional school this fall. Yay for apartment hunting craziness.
The vendor stuck with his original offer (he would pay half the cost of thinning and repair) and made it very clear to me that the issues were caused by me. Apparently these are issues caused by laying the knife flat on the stone and thinning. I'm sure as hell that he did not believe this and was trying to pull a fast one on me. Why would he offer to pay half the cost of repair and thinning otherwise?
Anyways, continuing on, Shaun F offered to do the work for the amount Mark offered him and return shipping. He received the knife last week and shipped it off this weekend so I'm expecting to see it this Friday. Hopefully the issue has been corrected, but my hopes aren't high.
After this, I do fully understand why people have such strong opinions about that vendor. It's left a bad taste in my mouth and I will stick with forum approved vendors from now on. One thing of note is that Shaun F was very responsive, accommodating and willing to help and in general, I found him to be a very pleasant person; I will post pictures of his work when I receive the knife. Until then, I've got my fingers crossed.