My spouse has done well on Paleo starting around 2009. He's added back more foods, such as legumes, rice and potatoes, as "resistant starches" and he's also added back sheep yogurt this past year. He's been experimenting with various fermented foods (the yogurt, kraut juice, lacto-fermented pickles, etc) and probiotics too in this past year.
In the past 2 years, he had a problem that and we finally sorted it out as histamine intolerance. We had to tweak our version of the Paleo diet to decrease the histamine a bit and also added specific anti-histaminic herbs and spices (mint, ginger) and that plus the probiotics seems to be helping. Smoked meats, aged sausages (salami) in small portions only!
Because of the colon pain - if you're interested in the probiotics and the fibers that "feed your friends," the Cooling Inflammation and Animal Pharm blogs are worth a look. For Paleo, Marks Daily Apple is a good place to start, but there are a ton of blogs and cookbooks out there.
I've been perfectly happy eating paleo with him and can easily feed guests or my entire family that way. Everyone likes it. I don't do a lot of "paleo" treats with almond flour, etc. I'm just not much of a baker. Baked apples though - yum!
I hope these are promising lines of inquiry for you and that you are able to get some traction with the problem soon. These diet changes are a lot of work and you want the effort to pay off! Keep us posted!