Nice reference!!!, I’ve never heard of Joe and Mac. Definitely gonna check it out. I see what your saying about the eyes, I wanted the art style to be a mixture of clay-mation style kinda like Chicken Run, Wallace and Grump, with a bit of modern fantasy style. I could always experiment and see what works best. 
As far as texturing i am just using Photoshop. Nothing special. I know how to use painter but i feel more in control with Photoshop. I like painter a lot (its awesome!!) but for this art style zbrush and Photoshop do the trick. I am not doing anything crazy with the specular map or pbr shader. i usually use flat spec maybe with a tad bit of roughness. but overall i use Photoshop for most of that.