I'm thinking that it was the wind that fed more air into the vertical smoker that caused the temps to run away. Normally that old POS is actually good for this kind of work because it runs very cold (normally) and the access door makes adding wood easy.
Anyway, not a big deal, just a tad disappointing, but there will be plenty more peppers this season. Plus, I still have some smoked peppers left from last year.
Jalapenos are traditionally smoked over pecan wood to form chipotles. I've been using plum for the last few years because I have a lot of it and it has a very unique bite. Almond would be fine, oak might work, cherry would probably be fine too. For various reasons, I would avoid hickory, mesquite & apple. Citrus wood would go unnoticed.
Since temperatures and times are dependant on the peppers, I think it's better to just explain the idea than give any definite numbers.
Start with ripe (red) peppers. Yeah, those fresnos weren't quite red, but close enough, also, fresno peppers are some of the few peppers that still taste good when you use green ones - them and certain varieties of thai peppers. Tear the stems off, try not to tear open the flesh of the pepper.
What you need to do from there is simply dehydrate the pepper with smoke. It's ok to make smoke for the whole cook, it's not going to hurt the peppers so long as they aren't dripping with tar and creosote. You also want to keep temps as low as you can to avoid burning (only use a few coals and just just keep adding a few freshly lit coals and smoke wood as necessary), below 200 if possible.
Large, thick, fleshy, watery peppers will take longer than smaller, thin peppers (DUH), and you just need to watch them until they are leathery/dry. I think the winds did me in on this cook, so instead of leathery & slightly pliable, I few right past that at the end and went to burnt cracker.
To give you a ballpark on times, habeneros cook quickly - maybe an hour or so. Thai will cook quickly also if they are in a perforated basket, if they are on foil, they'll take longer. Fresnos, 4-5 hours depending on temps. Big thick watery jalapenos, longer. Opening the lid every 30 minutes to peek and every 10 once you get close isn't any big deal, it's not like a hunk of meat where doing that can mess up your cook.
Oh, BTW, can't use most supermarket peppers because they are usually coated with food grade wax.
---
Oh, and you have to smoke an egg while doing it - it's a tradition...
Take a raw egg, use one of those thingies that punches a hole in the end of the shell where the airsack is or just use a thumbtack/pushpin, then put it on the grate. After about 1.5 hours, it'll look all brown and coated, pull it off, let it cool, crack it open and treat like any other hard boiled egg.