I'm not saying this makes everything crystal-clear, but here you go.
Keymaker: There's a building. Inside this building there's a level where no elevator can go, and no stair can reach. This level is filled with doors. These doors lead to many places, hidden places, but one door is special. One door leads to the Source. This building is protected by a very secure system. Every alarm triggers the bomb.
Vector: Bomb? Did he say bomb?
Keymaker: But like all systems it has a weakness. The system is based on the rules of a building. One system built on another.
Morpheus: Electricity.
Keymaker: If one fails, so must the other.
Niobe: No electricity, no alarms.
Ghost: But you'd have to take out a whole city block to kill the power to a building like that.
Keymaker: Not one, 27.
Vector: 27 blocks?
Keymaker: There is a power station. it must be destroyed.
Niobe: There must be some kind of failsafe.
Keymaker: Yes, there is an emergency system. The core network of the grid must be accessed. The emergency system must be deactivated.
Soren: Then what do you need us for? Neo could take 'em both out easier than we could.
Keymaker: There's no time.
Niobe: Why?
Keymaker: Once the door is unprotected, the connection will be severed. But another connection must first be made.
Ghost: How long will that take?
Keymaker: Exactly 314 seconds.
Soren: Just over 5 minutes.
Keymaker: That is the length and breadth of the window. Only The One can open the door, and only during that window can the door be opened.
As far as your hovercraft question, I don't think they had terribly many. And many were lost in the failed ambush that we do not see, but hear about at the end of
Reloaded. The EMP is set off too soon, and the machines wipe the floor with them. Bane is the only survivor, and he's in a coma. (And the Neb... Nebb... Nebe... Nebu... Morpheus' ship was destroyed near the end of
Reloaded also.) Lock - the guy in charge of Zion's defense system - had been ordering the few remaining ships back, so the crew could help defend Zion. At that point, I don't think there were a sufficient number of ships to last any time whatsoever if they tried to fight the machines outside of Zion.
"Hi, I'm Naomi Judd, and I'd like to sing you a song..."
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