m4gnificent_b4st4rd: That is some awesome progress

Tho you seem to make many assumptions about stuff being difficult in Radiant, it's not: I could also make that octagon thing in about 30 sec with the brush cylinder tool or patches, it's also possible to move vertices from several brushes at the same time (to adjust the height of that building), it's also possible to merge brushes together into 1, as long as it stays convex.
Also, how well (if at all) are quake 3 shaders handled?
About the edges not lining up: this happens when the shared vertices for 2 faces don't line up to grid (because 1 or both are on a weird angle), (the Radiant grid increases 2x on each 'level', (0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256 units), as opposed to blenders 10x increase). I'm not sure if you need to keep vertices on 0.125x or whether you could use any 3 decimal points like .001. You could probably figure this out from a .bsp. I have always managed to avoid this issue by splitting brushes into smaller ones, that only have triangles (not quads) visible.
Have you figured out detail brushes yet? If not, get to it! And make sure to cover all unseen faces with common/caulk.
The .map you posted earlier didn't have "// entity X" in front of every entity, only the first, re-saving with radiant fixed that tho.
Some limits you may need to keep in mind:
you need to keep your maps within +-65536 units (which is huuuuuuge, 2km in every direction (32units/meter)), or preferably half that;
IIRC brushes can't have too many sides, tho maybe that was a Radiant/compiler issue in an older version;
you probably won't ever hit this limit, but you can have at most about 900 entities (+64player slots, +buildings has to be less then 1022), although even that is too much with high bps.