I'll check the iron production again. Maybe I missed a bug somewhere.
The deep mine, near the barracks of the vanguard forces, can be entered on the management map and world map. Maybe you accidently try to enter the mine next to the construction guild? That mine was never accessible. If that is not the case, either check if your game version is the newest, or send me your save per mail to Naughty-Netherpunch@web.de so that I can check if it's an issue in the save for some reason.
The command center screen is also still accessible, so I really wonder if your game files are correct.
What level 4 upgrades do you mean?
The story will continue in this game. The next step is the "time skip" phase, which I have already started working on. A preview can be seen via the sparkling book in Ryen's bedroom. After the time skip, the big battle against Raziel and all connected events will take place.
Transfering on android sadly doesn't work due to how the .apk is created, but on all other systems is simple copy&pasting of the entire www/save folder content.