Xan my man... we got problems. I'd planned to wait for a version with the pictures fixed before posting again, but there's too much stuff, and I think you should know about it ASAP, so you can get to work fixing it.
I wanted to keep testing, so I cheated... I looked into the game code to help me out where I needed it, so I could keep going. It's good that I did, because without that I wouldn't have been able to go forward, and I wouldn't have found some of this stuff.
(FOR ALL FUTURE PLAYERS, SPOILERS APLENTY PAST THIS POINT. YOU HAVE BEEN WARNED.)
The major bugs first:
-First off, once you gain access to the garage you can end the game without meeting any of the necessary criteria. Just go out and you escape. Nothing stops you from doing it, even if you have no codes, no vehicles disabled, no prep done.
-I also found another place where, as Blerk, you can get trapped. It's above the chem lab. If you haven't blocked the door yet, but you've mixed the gas, it tells you to leave the towel behind before you leave. But even after you drop the towel, it still says the same thing, meaning you can't leave at all.
-The motorcycle is, for all intents and purposes, hidden. You can interact with it, but it's not in the garage description, it doesn't appear in the places/items pane, and it's not included in the hints. Again, if I hadn't been peeking at the code, I'd never have known it existed.
-Even after disabling the tank, motorcycle, SUV, red car, black car, and ATVS, the garage still thinks I need to disable one more vehicle. If such a vehicle exists, I couldn't even find it in the code.
-Blerk never seems ready to leave. This may because the game still thinks I'm missing one vehicle, or it might be a separate problem entirely, but I've got all the other criteria (that I know of) met.
Some smaller issues:
-The "look at" button on your "gas spigot and valve" doesn't work. It says it can't see it, I think because it considers "gas spigot" AND "valve" as two items? I'm not sure.
-As far as I can tell, the mortar and pestle does nothing. It gets discarded at one point, which tells me you meant for it to serve a function, but all my attempts to use it failed. I was in the right neighborhood (the zinc), as that's where it gets discarded, but I never actually successfully used it for anything.
-For some reason, when you enter the commons, the room description displays twice, back-to-back.
-In the private office (the one you need the elevator to get to), there is an object in the panes called something like "Desk from hidden under desk". Kinda ruined that particular puzzle.
Also, a conceptual issue: you need to allow for a lot more variation in the commands the player can use. Sometimes it's just a matter of "use x on y" when only "use y on x" has been programmed to work. Sometimes "use" does nothing in favor of more specific verbs like "pour" or "push", but other times those same kinds of actions ONLY work with "use". It results in something very much like "guess the verb", where I know what I, and the game, want to do, but I have to find a particular phrasing to get it to actually perform that function. Going through and adding a bunch of command synonyms would be a real help to players.
(One particularly aggravating example of this, for me, is getting the napkin off the tray. "Drop napkin" doesn't work, but "take napkin" does? I get your reasoning after the fact, but it seems pretty counterintuitive in game.)
There's a really cool, albeit really tough, game under all this. But you need to do three things to make it what it can be:
1) Bug fixes (obviously).
2) Command synonyms. Seriously.
3) Hints, and I don't mean the hint system. I mean you need to use the descriptions to clue players where to go. Mention the stink of ammonia in the bathroom description without requiring the player to smell. Have Xan recognize a quote as being Sun Tzu. Note that the tube would be better if only you could find a way to shrink it. It isn't that your puzzles don't make sense, because they do... it's that there often isn't enough in the game to help the player connect the dots.
I hope all of this inspires you to fix the game up and make it perfect. I know it might seem like I'm piling on or being insulting, but believe me: if I didn't like what I've seen, I'd never have given this much time and effort to it. Hope this helps.