I make my own chipotles. If I need to add the flavor to something, I grind one up and add it in. I use mesquite for the smoke and jalapenos grow like weeds, so I figured I would just do my own. I smoke them raw and then dry them out. I've done it for a couple of years now and have been able to do about a years supply each year. Only problem is, they are becoming quite popular around my house, so the supply may not last as long as it did when I first started out. My house salsa has them in it and chicken or shrimp in a chipotle cream sauce seems to be a crowd favorite around here as well. Using them dried takes the vinegar out of play.That sound really good. Do you cold smoke them or roast/smoke them? I may try this with poblano peppers, one of my favorite ingredients.
I smoke them around 180, then dry them at 225 for 6 hours or so. I have done poblanos and habaneros as well, but the jalapenos seem to come out best. Poblanos are sometimes not spicy enough, it really depends on the growing season. This year was the first year in a while where my poblanos had some heat to them.