Subtraction actualy appears to create that so called "other crap", the colission errors, more often for me then when im just Cliping with the Clipper.
About the Light Mapping issues, never had such problems because i use a Proper set up for FSRad.

Anyhow, the Map Structure seems okey, its a sewer so its not uber pretty and has different textures all the time.
But some variations would realy improove it, Dont like the Lights you made that much.
Secret Rooms/Passages are nice but for somereason the ones you made dont realy fit imo.
Other than that a Okey Map in overall.