I have been following your story, but wanted to do a bit of research before I responded.
The ingredients in your previous food are this:
This is taken from the website of natural balance.
You have essentially COMPLETELY changed your Baby Duke's Diet.
Here are the ingredients in NVI Beef:
My theory is that you switched the food too quickly. Because of the completely different variations of ingredients here, it has given Duke a tummy ache. A bad one.
As far as the poo being fine and firm for (6?) days, that would be expected, as it really does take a few days for it to get through their system.
Let me elaborate on this, because many years ago, our bully Sarah (the highly allergic one) was fine one day, and the next day she was pooing like crazy. She could not hold it. The look of terror in her eyes was so sad, I could not get mad. The poo consistancy was different tho, like almost 'foamy'---because it was full of gas.....
I would give her 1 cup of food but she would poop out 6 cups. It was crazy, and yes there was a liquidy blood with it. After going to the vet, he asked me if I had made any changes to her diet recently. Well, I had switched her (slowly) from Iams puppy to Iams Lamb and rice- I KNOW YUK!!!! RIGHT???!!!! And this was about a week before this started happening. She was just turning 1 so I wanted to change her to adult food. Well, come to find out she was HIGHLY allergic to 3 of the ingredients in the food after we had blood tests done on her, Lamb being the worst.
My point of all this is that it does take time to see what happens with the food. I would also say that if it is causing any allergic reaction you may see poop consistancy of what I described.
So my theory is one of two things:
The food change happened way too fast, or you are giving too much of it per feeding. This is more than likely the case I think. This caused swelling in his GI tract.
The other is a possible allergy to one of the ingredients. Beef is considered a 'hot' food, many dogs do have allergies to this, but it is better than chicken usually. I don't think this is the case, however, because the poo was not that bad, and he was already tested for food allergies in the past (although they can develop later, so it is not impossible that he does not have any food allergies now).
So what now? What do you do?
Do the bland diet for a couple of days. Once things firm up, slowly start introducing the Nature's Variety into his diet.
Start with 1 cup of rice, and 1/4 cup of kibble. Do this for about 5 days and make sure all is still well. Then go to 1/3c kibble. (5 days) Then 1/2c kibble. (5 days) Then 3/4c kibble (5 days). Then decrease the rice amount to 1/2c (5 days) then none at all. Normally a food change should not have to go to such EXTREME measures, but this is to make sure there is no upset on his digestive system at all.
I don't think you should stick with the limited ingredient duck and potato because I don't think he is getting enough vitamins and protien. That food is used to try to identify a food allergy. Since he is not allergic to food, there is no reason he should be on this diet.
ALSO--- too much potatoes in that diet. I honestly believe you will see a huge improvement once you successfully make the switch to NVI, and hopefully in the end all of this will be worth the effort you are making. When this happens, I hope you will type up the whole story, and share it with others in the Dog Food and Nutrition articles section. Please keep us updated!
P.S. I also think it is unnecessary to give the tummy medicine at this point if his poops are improving and does not seem to be in any physical pain.

But it is good to know for future emergencies!