That sucks man. I'm sure that kava can stress the kidneys but I wouldn't think to the degree that it would look to your doctor as though you'd been exposed to a toxic substance. Do you drink alcohol or take any medications in the past couple of years? Over the counter NSAIDS can wreak havoc on your organs. And for what it's worth, do you drink lots of water and eat/drink plenty of electrolytes?
I take milk thistle almost every day and I have not had any bad test results or anything. I posted a good while back about getting pains in my kidney area. I cannot say what the cause of the pain truly was, it could have been kidney, muscle, or a spot where a possible intestinal blockage was creating pain. However, it did persist for a long time off and on and it got worse with dehydration. it went away on its own for a couple months and returned again for a couple months (not daily, but often) The pain has not returned since I started taking milk thistle, and it's been a long while. Its got studies backing up it's safety profile and efficacy in taking stress off of the body's detoxifying organs (Liver, kidney, gallbladder to some extent.) You should probably take a break from kava to get things sorted out but if you end up drinking more kava I think milk thistle is something that should be in every kava or alcohol drinker's routine.