Just wanted to say that I like what you are doing!!! So keep it up. I actually never thought about it, but FTL could work really well as a steampunk world.
I'm not sure I could help too much but one thing I thought I would share is that you can change pretty much every aspect of the UI (though it may take some work) , and more things are changeable on the boss then you might think. I know and can tell you how/what you need to change for pretty much anything, but I am not sure I can actually help out much myself, too busy
The backgrounds should be easy to change, you just need to find some sky images like faster than sound does. You can even change the "beacon map" images (which are now strangely found in the iPad folder) and what is interesting is those could be the only "top down" map images of the new "world" you are creating here. For the UI, making it wood textured or metal textured would look really cool in contrast with the sky background.
Anyway, this will take you a long time, but if you can commit to it and keep making those awesome ships you are making, you WILL be able to achieve what you are hoping to achieve in the long run so keep at it if you can!
By the way, love the bee ship. You can totally extend that into a wasp ship, mosquito ship, etc...