Most of that stuff isn't relevant at all; do a search on [error] to cull it down to the things that matter - there's 130 hits.
Of those, all those EDB errors are false positives; the game is reporting the fact that they have more than one upgrade option. It's not an "error" at all, and doesn't do any harm.
Most of the things it's reporting as missing are irrelevant vanilla files, which won't cause a crash. Even then, missing stuff is almost always defaulted to something else. Warnings don't matter.
This section is potentially problematic:
13:10:29.187 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1254, column 89
Volume is out of range.
13:10:29.187 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1254, column 93
SOUND_DB::read_sound: Invalid sound
13:10:29.187 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1256, column 11
SOUND_DB::read_sound: Invalid sound
13:10:29.189 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1257, column 12
SOUND_DB::read_sound: Invalid sound
13:10:29.191 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1258, column 12
SOUND_DB::read_sound: Invalid sound
13:10:29.193 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1259, column 12
SOUND_DB::read_sound: Invalid sound
13:10:29.194 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1260, column 12
SOUND_DB::read_sound: Invalid sound
13:10:29.196 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1261, column 12
SOUND_DB::read_sound: Invalid sound
13:10:29.198 [script.err] [error] Script Error in mods/EBII/data/descr_sounds_units_anims.txt, at line 1262, column 12
SOUND_DB::read_sound: Invalid sound
Even then, the game gets past it fine. I can't see a terminating error in there at all; if this was a CTD, the last line should be the error.
It seems to be some bizarre bug whereby the first generation always crashes for some people, but then the game should run fine after that.