Hey CM, I had the same problem for awhile, as both my smokers are used over and over and over again for MEAT! Two ways have worked well for me, dehydrate half way, then smoke, then dehydrate the rest of the way( preferred method) or if I'm feeling lazy, I will leave the pods whole, wrap the whole bundle in several layers of cheese cloth and put them up on the highest rack, and soak the shit out of the wood chips for maximum smoke in shortest amount of time, of course I never try to smoke more than a few pounds at a time for dehydrating, now if I'm making my smoked red habanero BBQ sauce, I smoke um up to pieces w/ the onions garlic and tomatoes, so I don't care how oily, or mushy they get they're going straight in a sauce!
Oh PS if you don't have cheesecloth, tinfoil works if you take a kebob skewer and poke a bunch of holes.
Oh dang I forgot to answer the other part of the question, fully dried pods will retain a hint of smoke flavor, but for deep rich smoky goodness, you need to have looser pores in the flesh, as they dehydrate, the skin gets super tough and the smoke doesn't permeate as well!
And speaking of invaluable tools, thanks to you and rocket man for the fermenting thread, I've made pickles and sauerkraut and preserved lemons and such in my time as a chef, but I had never made fermented hot sauce, now I do it several times a year thanks again!