We had a similar issue with one of our kittens, Oscar. He had a bit of a dodgy stomach from the day we got him, which we initially thought was caused by the change of food, but it turned out he had a bit of colitis, which we think was caused by worms. How many courses of worming treatment has Jupey had?
It took a tube of promax (probiotic which we got from the vet), a weeks course of antibiotics and cooked chicken diet (we're only just weaning him off the chicken) to settle his stomach down.
What do he poops look like? Are they gooey or liquidy? (lovely topic eh!) We noticed Oscar's were gooey and had a bit of mucus in, which aided in the diagnosis of colitis, which is apparently very common in kittens.
As for wet food, natures menu has 70% meat, but they only do chicken flavour in the kitten, that's around 5.70 for 12 pouches and Jollyes sell it. Ours weren't too keen on it though so we're stuck with 24 pouches of it with the kittens not liking it.
We thought it might be food as well, but we're integrating whiskas back into his diet and it doesn't seem to be affecting him in that way yet (fingers crossed).
As sharky said, James Wellbeloved is also a good food, and it's a complete dry food, they are naturally hypoallergenic, and we feed our two the ocean fish flavoured.
Anyway, I'm no expert and we were never 100% sure what caused Oscar's colitis, but I just thought I'd let you know all the information which I got, as it helped me a lot in diagnosing him in the first place.
Hope he gets better soon!