The lightmap is more or less a big, compiled texture containing the lighting info for all surfaces on a map.
AFAIK there is an ongoing effort to detach the lightmap from texture scale, I do not exactly know how far the code is already. (sizeless textures branch)
I like your map & the idea & complexity behind it, and as mattn said - it would be no problem to split your map in 4 parts for example and use the RMA code to assemble it back (without actually making the assembly random, just putting the parts back together in the correct order).
This will completely eliminate the lightmap problem and you can keep up the good work on details, without worrying too much about complexity and scaling...
Take a look at alienbase, and how H-Hour used the RMA code to assemble it.