Couple of things...
Firstly the hull cannot and will not be repaired untill you return to your home base.
If systems are damaged beyond repair ... well they wont get repaired. Currently there is no way to know they are beyond repair except that they dont get repaired
If in fact your diesels are damaged beyond repair its time to load up a previous save.
As mentioned make sure you dont have silent running called for as they wont do anything while its active.
Lastley make sure you havent been at battle stations for 3 days
turn battle stations off and let the crew get some rest.