Ok, ive played the mod, and i know how to get past the part where you're stuck:
What you need to do is go close an open zone to unlock other zone consoles.
In other words: if zones 1 and 2 are open, and i want to get to zone 3, i must first go close zone 2. Then zone 3's console will be available. Once i open zone 3, zone 4 and 5's consoles will be available. If i open either zones 4 or 5, all the other consoles will become unavailable. I choose zone 4. I must then go into the mines through the zones i have just opened, do what i have to do there, and then come back to the control room. Now i want to go to zone 5, so i close zone 4 so that the zone 5 console becomes available. When zone 5's console becomes available, i can then use it and open zone 5.
It may be easier to open a zone, and then explore it one by one rather than to do 3 at a time.
^ Does this make sense? I can post screenshots if you need help.