I'm really glad that in general she has been doing better and a cause was found for some of her problems.
Going by your description, you may have an immune compromised dog that is going to just be like this, which may pose an o going challenge (and I'd inform the breeder). On the other hand perhaps she will just pull through this phase and these various illnesses -- sometimes sickly dogs get a lot better in adulthood when their immune system strengthens. She is still terribly small though.
One thing you might need to seriously consider -- if the kennel guy (I am pretty sure I know who this is) is actually able to get her to eat with no problem -- is that much of her refusal to eat is behavioural and is primarily something she does for attention and occasional interesting tidbits from you, even to the extent of weight loss and putting her well-being at risk.
This could well be a possibility given how you regularly are rotating foods and trying to lure her to eat, and the fact that she will suddenly eat a new food, then stop again. This is pretty classic behaviour when there's a learned behaviour issue going on. The difficulty is how to tell.
If she eats when kennelled it will be because she knows she gets her food and that's it and she can't create any interesting attention around the event. There's no one to play up to and no one inadvertantly rewarding this very unwanted behaviour.
I'd have a read about this issue here and follow the directions to a T if she comes back with the report of 'no problems eating'. This is a really common problem and very rarely a dog will carry it to real extremes.
http://board.cavaliertalk.com/showthread.php?t=24168
It may be that it would be better to have your husband feed her or whoever feeds her least, to cut the association with not eating and any possible game-playing.
Also like Lani I am still a bit concerned that the vets didn't order these tests and other long delays in seeing some of the things you have been describing. It isn't your job to have to demand tests be done -- they should be identifying and eliminating all possibilities and this type of test to me would have been one of the very first things I'd have done as well as giardia --these are vet basics, not things clients are supposed to be asking for. I'd be inclined to get a fresh pair of eyes and a second opinion. Made some suggestions when we spoke, or PM me for further detail again. I'd do that before UCD.
Finally: I would definitely not leave an ill dog in kennels. She sounds from your posts like she is truly just barely surviving and has been at death's door only recently -- and has several quite serious issues and is on a lot of medication. A kennel is a serious slam to a weak dog's immune system and she is barely larger than a 2 month old puppy. Many kennels will not accept an ill dog as well -- as a risk to everyone else's dogs. It isn't the issue of how good the kennel is; it's that in such an environment she will be exposed to lots of potential illness from lots of dogs that could be carrying anything. A healthy dog would be OK (yet even with healthy dogs, kennels are a common source of illness!); an ill dog should definitely not be left in a kennel. I would home board or have someone you know mind her or if a vet's does boarding I'd leave her at a vet practice for daily care.