For some reason, the metal bars on the small elevator and along some stairs beside that same elevator has little reflective dots that glow in the dark.

It's not a bug. It is impossible to change reflections in real time depending on light switched off or on, in Source Engine.

There doesn't seem to be a way to get the lever in the room so that you can open the gate...

There is a lever in opposite room in cabinet. You have to put it in lever base

I mean, I can't figure out how to disable the forcefield that's blocking the lever from being taken through the doors. It looks like there's a missing dial, but I didn't find anything that could go there...

There are three holes in window. You can use them to get lever into that room :)

Let the map creator be the only guy who reads this spoiler
When you want to get an access code to the door from a man behind a wall, there's a chance the paper with code gets stuck in a room behind a wall and a player cannot reach it. This occurs only when the gap in a brick wall is obstructed or a player is too close to it.
This small detail may ruin the entire puzzle

Thanks for that, just updated map and fixed it.

For some reason I couldn't get the door code to work. I even tried zooming in to push each button, but no dice. Ended up having to unlock the door via context menu.

The train map in the junction box doesn't show,

Originally posted by ~Lightwλve~:

For some reason I couldn't get the door code to work. I even tried zooming in to push each button, but no dice. Ended up having to unlock the door via context menu.

Sometimes when clicking buttons it is easy to miss but I can’t belive it didn’t work for you. There is no way I can improve it.

Originally posted by Maxis:

The train map in the junction box doesn't show,

Map shows always after connecting plug to power socket. Did you do that?

Originally posted by Admirally:

Originally posted by Maxis:

The train map in the junction box doesn't show,

Map shows always after connecting plug to power socket. Did you do that?

Yes

Originally posted by Maxis:

Originally posted by Admirally:

Map shows always after connecting plug to power socket. Did you do that?

Yes

Update, got it working but had to cheat a bit using noteclip and cameras

After watching your video, I realized that: 1) I have very bright stripes that block the train branch 2) The branch itself has moved up, which is why only a piece of the entire path is visible.