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Neil,
Here is some more information on how the TDR setup works. It is a bit "hand wavy", but its been a long time since I really worked with this kind of calculation.
First, the Fourier transform provides a connection between the time response and frequency response of a system. The time response is often described by the impulse response, which is the response of the system to a very narrow pulse. In theory the pulse is infinitely narrow, infinitely high, and has finite area under the amplitude/time curve. The theoretical impulse has infinitely high frequency components. In a practical system, we can use a reasonably narrow pulse as an input to a system, but for say, a 1GHz response, you need something like a 350ps wide pulse to stimulate it. Similarly, you need a 1GHz bandwidth system to look at a 350ps pulse. A 1GHz system (filter or whatever) can be described by how it passes a 350ps pulse or by how it passes (amplitude and phase) a range of sine waves from 0 to 1GHz. The Fourier transform relates the time description and the frequency description. If you know one, you can compute the other with the Fourier transform. In practice, we use something called the Discrete Fourier Transform (DFT) because we have discrete samples spaced out in frequency or time. Further, the DFT is implemented as the Fast Fourier Transform (FFT) because it is computationally efficient. (The FFT was figured out when I was in high school, so it is a recent development, although some folks say it was anticipated by Gauss.)

Conventional TDR:
In a conventional TDR system, an impulse (Tek 1503) or step (Tek 1502) is transmitted into one end of a cable, and the system looks for reflections. A perfectly terminated cable has no reflection, a cable open at the end reflects a positive signal, and a shorted end reflects a negative signal. An improperly terminated cable reflects something between the short and open signals; the termination value can be determined by the sign and amplitude. A piece of 75 ohm cable spliced into the middle of a 50 ohm cable produces reflections, and in the case of step input (Tek 1502) the reflections can be viewed as showing the impedance versus distance along the cable. For impulse input (Tek 1503) the interpretation is not so simple, but it does clearly show where discontinuities are located. Integrating the reflected impulses can produce a display equivalent to the reflections you would get with a step input. The distance resolution is something like the step risetime or impulse width times the speed of light. If you know what you are looking at, a cut cable end, say, you can get much better resolution, but it is hard to figure out arbitrary faults with dimensions less than risetime*(speed-of-light).
VNA TDR:
With VNA TDR, a series of sine waves are applied to the cable end and the amplitude and phase of the reflected signals are measured. Higher frequency applied signals get bigger changes in phase for a given distance to a reflecting fault and thereby allow better resolution. Wide frequency spacing of signals shortens the maximum unambiguous measurement range. Signals spaced, say, every 30MHz (3000MHz/100 steps) cannot distinguish reflections at 33.3ns and 66.6ns. For VNA TDR, the FFT converts the amplitude and phase of the reflected frequency signals into the impulse response of the reflecting cable. Integrating that impulse response converts the display to the reflection response to a step input, which is the Tek 1502 style of display.

Setup reasoning:
"Set stimulus for a wide sweep, say 50kHz - 900MHz or more."
High frequency gives good resolution, but shortens maximum length

"Do an SOLT calibration at the desired measurement point (if not already done)"
VNA works best if calibrated

"Set TRACE 0 for Real format"
We want linear (not log) input to the FFT. But "LINEAR" format looses polarity (short vs open) info

"Turn TRACE 1 off"
Reduce clutter

"Set TRACE 2 for Smith "
Smith markers let us read off cable impedances directly

"Turn TRACE 3 off"
Reduce clutter

"Turn TRANSFORM ON"
Convert from frequency to time representation

"Select Transform LOW PASS STEP"
I like this format, gives cable impedance directly, similar to Tektronix 1502 TDR

"Adjust ELECTRICAL DELAY to move the displayed window to the desired location along the cable"
This extends the good resolution to greater lengths, still subject to the ( 1 / (frequency-step-size)) limitation

The resulting display should be similar to that on a step-type TDR like the
Tek 1502. With 900MHz max, the display width is about 43ns, with 3GHz it is about
8ns.
Impedance along any connected cable can be read by moving the marker to the
desired time (distance) and looking at the Smith chart marker values. You need to mentally add the
ELECTRICAL DELAY to the marker time to get the actual delay.

" Save via the CAL menu when you have it all set up."
Saving is a good idea