Its always been a problem starting a map from inside hammer after a compile, just tick the flag "don't start the game" in the compile parameters dialog.
You can set a trigger_hurt to negative damage, and set damage type to generic, in that way it won't make a sound, keep in mind that it will heal players the amount set per second, so setting it to -999 causes them to get 999 health more per second.
To place models add a monster_furniture, but it won't be solid, so create a clip brush around it. DoD has an entity that makes solid models ingame. Make sure the standard wads are set up in hammer.
Xen healing pools are created by trigger_hurt with negative damage and damage type set to generic. As for your latest problem, either use texlights or don't name the light, light_spot and light_environment entities.
Doesn't it cut up everything into small brushes of 1 unit thickness? If BSP2MAP and WINBsp are merged we would have a good decompiler, but that would suck for honest mappers :P.
For #2 you should use a trigger_once placed on the spawn of either team, make it target a multi_manager which toggles the sound and off again when you want to, unless the sound doesn't loops.
There are a lot of brushes badly designed, there are brushes outside of the world, brush-based entities without a brush assigned to them. I think it would be better if you build the map all over again, unless it took a lot of work to build already.
You're making a map for condition zero, and you post this in source discussion? Also, it looks like there are several brushes leaking or in eachother, try going to the co-ordinates and see if there's a hole in the map or a brush inside another there.
Something i found out when i was making a jet fighter for my map: func_train works with path_track. It doesn't rotate, but it follows the path as normal. I just wonder if Osprey's would work with path_tracks.
You could use teleporters to make the player get an angled view and movement, together with trigger_push this would make it look as if the player was walking on the sphere.