Given that there are 6.5 billion people in the Matrix, and given that despite the population density of these farms being quite high compared to current human settlements that the farms must occupy quite a lot of space (I'm estimating they must cover at least a thousand square miles.)
Your estimates are off by a very large margin. According to this website, if you took all 7.3 billion people in the world (circa March 2015) and stood them shoulder-to-shoulder, they could fit in an area 27km squared (16.8 square miles.) And since that source is talking about everyone standing on the ground, it's not factoring in the space savings of stacking them vertically.
We know the machines don't pack them in quite that tightly, but even with the distance between pods seen in the film, 6.5 billion people could easily fit in an area the size of a major metropolitan city (like New York.) We don't know exactly how fast a hovercraft can get from point A to point B, but I imagine they can cover that area and move to a specific point within quite quickly indeed.
how did the Nebuchadnezzar know where to find Neo's pod in the real world?
The red pill allowed them to interrupt the carrier signal that kept him stuck in the Matrix, and presumably to pin-point his location in the farm. You can't interrupt a specific signal until after you've identified what it is. You can jam a wide band of signals all at once by broadcasting a jamming signal, but that's not what they were doing to free Neo, otherwise they would've interrupted a lot of people's carrier signals at once (and likely brought the machines down on them as they would notice the disruption.)
Given that they have already identified Neo's specific carrier signal before giving him the red pill, they could also trace it, which would at least tell them which farm he was in. The pill then allows them to find his precise location in that farm (which is probably not bigger than a major city, as above) and the hovercraft can zip over to wherever he comes out since there's no traffic to speak of (barring sentinels.)
I assumed part of the purpose of the red pill is to disrupt the person's input/output carrier wave, which I took to mean they were using the disruption to find the person.
The disruption does not allow them to find the signal, it only interrupts the signal, so that the person is forcibly flushed out of the Matrix. Finding a signal can be done without interrupting it. Given the way people need to reach a phone to get into or out of the Matrix, "finding Neo's signal" is most likely what they were doing when they went into the Matrix and searched for Neo therein.
Even if the Nebuchadnezzar knew where Neo was ahead of time, there still must be significant travelling time involved back and forth between Zion, which isn't referred to at all.
The Nebuchadnezzar didn't wait in Zion until Neo's signal was interrupted. The ship was already in the vicinity of the body farm (after having determined which farm it was by locating Neo's carrier signal.) They only needed to travel from their hiding spot near the farm to the specific location where Neo came out after the signal was disrupted. As such, the distance between Zion and the farm is not relevant to the scene.