Oh, that can't be fun...
Changes in diet can cause tummy upset. Were they getting a different dry food at the shelter? And have you been giving wet and dry food from the time you got them?
It could also be a food sensitivity, if there is something different in one of the foods he's now getting. Grains, chicken, and fish are among the top allergens for kitties, so if any of those are in the foods, I would try eliminating one at a time to see if that resolves the problem.
I would also get both dewormed, as you wouldn't necessarily see all worms in poo. If the diarrhea doesn't stop, next would be a vet visit to check a fecal sample and you may want to also do a full PCR panel for diarrhea, as it can detect other parasites that wouldn't necessarily show up in poo.
In the meantime, you could give just a teeny bit of plain canned pumpkin to see if that firms up the stool a bit.