From the two walkthroughs - Very interesting looking game.
I like the idea of theme music/sounds that many areas and events seem to have. And the sudden scary sounds that randomly pop out at you from "nowhere". It helps give the game a feel. You've done a great job there.
Pretty funny how the men's room was behind a force field - hahaha!
I can see why though, there was a control room with it. One "goof" though - there's no way a prisoner in a straight jacket would be in that men's room. If a zombie was present in there, he'd have been one of the control room workers/guards.
An idea - don't know if this is possible with FPS Creator (well it probably would with some script-editing)... Have the taser aggravate and strengthen the zombies, make them more aggressive and dangerous... a Frankenstein effect (it could be like zombie-health kits). They could be nicknamed (by the pre-zombie guards/player) as zombie super-chargers. Perhaps the guards made that mistake too, against the ones who turned first.
Also the door sounds don't match the room type in many cases. They sound like small house closets, rather than large concrete areas. There are sites that have free sound effects for games. I'd also say have more varieties of zombies instead of just the one dude, including some guard and scientist zombies. The one zombie dude's sounds are pretty funny though!
How does a giant "boss" fit into the storyline? I've never understood why people always follow the script of having a "boss" at the end of each level. That was probably left over from '80s games, where the scope of the game had to be small and simple.
I guess my biggest comment is to remember the storyline, and organize the game around it, rather than just having an abandoned place with a few zombies hangin around. After those levels, the story really never unfolded, or seemed to exist. Something happened there. What? Shouldn't a significant part of the ongoing game experience be discovering what that is, by noticing the evidence of how things were left? Not necessarily to "solve the mystery", but just to see pieces of it (and let the player draw their own conclusion, for a more realistic virtual experience. If you do it well, players will end up debating their opinions and spinning stories about it later in the forums of your game
The bigness and details of your map are excellent! Including the ocean sounds outside, again helps give the area a feel to it (you may wanna turn the volume down on that one a bit to a more background-like level).