A positive update.
I spoke with Yafe's breeder tonight. It was a very positive experience and he set me at ease on a lot of issues that have been brought up here, as well as had some good ideas.
First, they run a pretty tight ship and they test for pretty much everything under the sun (including Nido - Zina10).
Secondly, he agreed that the RI should have been significantly better by now. He recommended asking the vet for a different antibiotic that a bordetella RI is sensitive too (which he offered to pay for). I have already emailed the vet and expect to pick up another antibiotic Monday afternoon. This saves the stress of transporting Yafe hours in the car, an exam, etc. I am very confident that we are dealing with an aggressive RI and not some crazy virus, etc.
It was a good communication and I feel that he has both Yafe's interests at heart and mine as well.
I'll keep everyone in the loop on what is prescribed and how it goes.