To answer your first question, Yes, I believe in order to start filling up the Engine Bay meter it needs to be repaired by an item in a later season (Though you can just ask us on the forums to help fill it up as many of us have already completed the quest and Engine fill shares among everyone. Though, to be fair, I don't know if it shares with people who have not completed the quest, though I think it does.)
To answer your second question, Collecting any extra Aether crystals is impossible. As of the update, there are other forms of crystals, (Like sapphire ect.) but none are Aether, and therefore, none can be used to build other meters.
I hope this answers your questions. If you have any more, feel free to ask.