I'm sorry I didnt read your opening post at all well did I ?
It seems really clear to me that your looking at a scripted solution since you have all the data you need its just a conversion job and a prettying up job. My little script I posted just does black and white squares but you can convert those into real nice dungeons. I'll edit some links in, in a mo but RobA has his dungeon map prittifier script for Gimp and I use some homebrew solutions too.
So if you have this information already then it can be turned into nice high res bitmaps without too much fuss and I do think that once the format has been translated correctly then you really might well be looking at doing your 40,000 maps overnight. Well maybe over two or three nights anyway depending on your PC capabilities
For example I can convert a black and white map into full textured one in about 10 seconds. So if you can get your data into a format that can make a set of black and white masks then I can make the bitmaps.
So.... looking at your ascii maps, what do the symbols mean ? Can you take a bit of one map, post the ascii for it and maybe sketch out with a pen what that might look like, or at least describe in detail what were experiencing in that sector.
From where I am looking at this point its not all that difficult a job. (Not that I don't have about six billion other jobs like that to do but hey...). Its not just me that does a lot of scripting here tho so you might get more interest too.
Edit:
Rob's
http://www.cartographersguild.com/showthread.php?t=2759
Mine
http://www.cartographersguild.com/showthread.php?t=2659