PMd you I'd post here in case this info useful for others. You were 99% on right track: just found a few problems which affected export.
1. Some of your textures weren't in folder/path Max was expecting them. I'll be sending a script which can help with relinking missing textures, but as a general rule good idea to keep all working textures/LM in one place: I usually put them in a High folder in project folder.
2. One of your objects was expecting the wrong texture: one called enviro5.ifl rather than enviro1.ifl. Easy slip but always worthwhile double-checking all material names.
3. One object had a lightmap but it wasn't rendered into ch 2, which can throw out max3 export. Again, easy enough in material editor to doublecheck all textures have lightmaps, and channels.
4. You mentioned some black areas in lightmapped bridge. Those are areas where light isn't really getting to them, and can be checked on UVW maps. Solution is either to 'paint' in light on lm texture, or adjust lighting so those areas do get hit. On pics below, I 'painted' in one liftdoor and left other as is.
Once sorted those issues out, BFFd to max3 then NIFd into game with red alert gamma setup. From first pic below, your original lighting quite nice, but once you go to red alert bridge too dark (common problem I have). I boosted all the lightmaps by half, which are remaining pictures. Had redmaps and yellow(blue)maps from previous experiments so thought would try them so you can get a sense of how bridge will look.
In a nutshell: lightmapping is a drudge and pain in the a**
