Hi Bim, don't know if you already found your answer, but you can use an LUA fog machine to generate clouds - this is actually covered in the advanced.txt file in the level design documentation (I believe).
However; there are a couple of things you should be thinking about regarding what you are building.
1. Existing work - there's already been a lot of work and discussion around dwarven branches. Just look on the dev wiki (
https://crawl.develz.org/wiki/doku.php?id=dcss:issue:2359 and
https://crawl.develz.org/wiki/doku.php?id=dcss:brainstorm:dungeon:branch:dwarf:dwarven_fortress). It seems to me from some of this that a lot of development has already been done, but I can't find seem to find the fork, and nothing seems to have happened in the last year. You might want to contact some relevant people and find out the current status of that work, so you can contribute your level design to that, instead of trying to get a whole branch started by yourself (which is a lot more difficult than simply mapping just one level).
2. Crawl branch development cycle. The devs do not typically want to insert an entire branch fully completed into the game. Instead, ideas are first developed as "Portal" vaults - Spiders Nest is a very current example of this. Once the portal is well developed and deemed balanced and interesting enough to expand to a full branch, things might go that way. So you should perhaps be looking at creating a number of smallish and interesting portal vaults around this theme and getting some feedback on them, I think you'd be much more likely to get something into the game on a reasonable timescale that way.