1) Fact#1: Some of weapons what placed on maps are not exist in MP mode of game, example in village2.bsp you can found "weapon_sniperScope" what can work only in SP mode. Solution: rewrite this block with hex-editor program (do it carefully to not broke file.)
Fact#2: Weapon models in MP mode didn't have a pickupp version. I do not know if this is provided in the engine code? but it's can be easy verified. Solution: take pickupp models of weapon from sp pak and past in new pack with mp_ prefix in his name.
2) Sounds of doors writing in door entity in Radiant editor, if it's missed - it's not possible to add in compiled version of level, .bsp file. I look on boos2 level throught hex editor and all doors don't have writed sound line. If you have acces to level source .map, you can fix it, but not in .bsp file.
3) .pk3 filetype is basicaly just renamed .zip archive, more info about packing resource you can read from
KatsBits tutorial