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You can't safely disable your mods and load a save that had those mods. Often that will break your game even worse.
Normally using the network scanner opens the doors to the relay chamber.
If you are Banished you should be able to use the Emergency Relay button on the desk console in front of the door (in some quests but not all), or just walk in to the chamber.
If you are not Banished and do have the courser chip from Dr Li then you just use Fast Travel, no specific action inside the Institute is needed.
From the sound of it maybe you have not yet got the chip from Dr Li in Advanced Systems?
That does not work. That does not clean your save.
Most likely whatever is wrong is baked into your save forever. You should enable all your mods, load a save before removing the mods and seek solutions on the nexus descriptions, posts, and bugs sections for mods that are likely causing the issue. There may be a compatibility patch or console work-around.
And yes you need to start a new character, disabling mods that were baked into a game is unreliable and unpredictable.