Vomiting, regurgitation and soft stool

[jeanne & Lilly]

I hope I can make this clear, I'll try to be brief, but give enough information to get help.
Lilly will be 2 yrs mid January. She ate Honest Kitchen Preference for over a year. With Preference, I cooked either chicken or turkey breast, then switched to (10% fat) ground beef. The switch to beef was about 3-4 months ago. Suddenly a few weeks ago, she started skipping midday meals, then when she did eat she would regurgitate, or vomit after eating.
Without going into her day by day diet, if she vomited, her next meal would consist of beef, rice, sweet potato, or just plain rice. If no vomit (or regurgitation) in 12 hours, I'd add a little HK to her next meal. Once again food came back up. On the 4th day of this we went to the vet she did X-rays to R/O a blockage. There wasn't a blockage; she chalked it up to just a sour stomach, and of course she tried to sell me their crap food.
The vet suggested that Lilly eat rice and beef for several days. When I believed everything was back to normal I reintroduced HK, once again regurgitation; came to the conclusion that the vomiting and regurgitation were directly related to the HK, so no more HK.
After researching for a new food, I went with Orijen Regional Red. A very small amount went into her rice and beef. We got up to 1/4 cup but if I increased it a small bit, her stool was almost liquid. As of yesterday she is back on rice, beef and sweet potato. I didn't log her stool during this time, it was sometimes normal sometimes soft.
Also after the first episode, Lilly started biting and/or licking her bottom. So now I'm thinking maybe she has a parasite?
Should I just bring a stool sample to the Vet tomorrow? Or should I bring her in for testing? But what kind of testing should be done?
I should also mention she was bathed and anal glands were expressed the day after the X-rays were done. The very next day she started to smell. At first she smelled like popcorn, now she stinks like dirty shoes, socks and feet! The odor is all over, but strongest at the back of her neck, not in her ears.
Again, I hope I didn't jump around too much and ya'll can make sense of what I'm trying to say.
Thank you in advance for your help.

[jeanne & Lilly]

Yea! Today Lilly's stool was completely formed, a little soft but formed! I am a happy Mommy.
I'm guessing after week of normal stool, I can reintroduce HK?

[Karen, Jasper and Jackdoodle]

Yes, that sounds about right. Keeping fingers and paws crossed here. 

[Jane, Guinness and Murphy]

Me too!

[F, Calla & Luca]

Me three.

[jeanne & Lilly]

Thanks to all!

[jeanne & Lilly]

Ok, Lilly is on day 8 of normal BM's. Should I slowly bring back HK as if it were a new food?

[Jane, Guinness and Murphy]

I think that would be fine....but go slow.  Let's see if Karen agrees.

[Karen, Jasper and Jackdoodle]

Yep, I agree. Go slow, and make only one change at a time. 

[jeanne & Lilly]

Thanks Jane and Karen

[jeanne & Lilly]

I thought I was going slowly reintroducing HK Preference. First 2 days 1TBS 2x day, day 3 2TBS 2x day and we were then back to soft stool. Days 4 and 5 back to 1TBS 2x day for 2 days and things continued to get worse. Saturday would be the last day she had HK. Yet early yesterday she pooped in the house, she has never ever done that before and we've had her since she was 8 weeks.
2nd stool yesterday and stool today are perfectly normal.
Did I make the changes too fast?

[Fitz & Henry]

Oh this whole conversation is freaking me out... We are now getting ready after the holidays to move forward with the specialist for Henry. The blood results show no immune compromise situation, so now they want to do an ultrasound, and endoscopy. All this to check him regarding the continued Giardia and his intermittent vomiting.
If I didn't know better, I'd say he has reflux or GERD. It reminds me of a baby who drinks a bottle and then it pops right back out. That doesn't happen always, but it does happen a bunch. If he gulps down water first ting in the am - he throws it right back up. If he gobbles up too much snow he throws it up. I've seen him eat his dinner and then 15 minutes later the whole thing is a pile on the floor. I'm not sure if it's from the metro.... Or he's just sensitive .
But it's sounds like they all have similar stuff....

[Karen, Jasper and Jackdoodle]

Did the blood work include a GI panel? That's the only blood work that is useful for diagnosing an inflammatory GI issue, and most GP vets don't run them. JD's didn't, although they said they did full blood work. It would have been sent out and taken several days, and it would have cost a few hundred dollars.

What you are describing is what happened with JD. It turned out that the inflammation in his gut was so severe that he had pyloric stenosis, and that's what was causing the regurgitation. 

The endoscopy is the only way to know for sure.