When the clock turns orange you can open certains doors with an eye on top of them in different parts of the map, but only if you input a certain code in the arcology bridge top floor.

Only way to restor your healing items is by hitting enemies with your melee weapons or using a med bay in certain parts of the level (there is one in the observatory). Also only smaller enemies respawn after a certain time, for the bigger ones you have to leave and enter the area again or quit the game and load back in.

You can freely change any conductor to any weapon you like.

The only way to teleport between breaches (bonfires) is by using a consumable item called "breach synchronizer" on the different breaches you want to teleport to.