You're close, but you still have a misconception. We don't actually measure the position of anything, because position is an abstract concept that would require infinite precision to measure. What we actually measure is counts or events. It just so happens that locality in spacetime means that two events are distinguishable when they occur at different locations. Consider the examples raised so far:
You pass it through some kind of electromagnetic field, it strikes a photodetector (e.g. a CCD), and you back-calculate out the momentum of the particle by how much it curved from a straight-line path.
What you measured isn't the location of the particle, you measured "1 electron hit this element of the CCD". You can infer much about the position from what you know of the structure of the CCD, but the pixels have finite sizes.
You use a Stern–Gerlach apparatus and note which way (up or down) the particle curved. Again by looking at the position of where it struck a photodetector.
Not likely. I did Stern–Gerlach in an undergrad lab, and we used a movable wire shielded and watched how the current changed as a function of position, iirc. In other words, we measured current, fundamentally counting the rate at which electrons passed through a circuit element, and couldn't localize the atoms better than the width of the wire.
In the old days, they just accumulated the metal on a glass plate, and looked at how the opacity changed.
You figure out the frequency of an emitted photon by its spectral lines -- once again by measuring the position of these lines relative to some axis.
I think you mean after dispersing the photon off of a grating or through a prism, right? Same criticism: you count photons and infer position. You could also measure the energy using calorimetry: you shine many examples of the photons on a sensitive thermometer and see how much the temperature changes. On old school thermometers that means measuring how much the surface of some fluid, like mercury, changed. In more modern thermometers (e.g. thermistors and thermocouples) this becomes a difference in voltage or current. Both of those measurements are done by counting/timing these days.
In fact, the only tricky examples I can think of are situations like radio and static electric fields, where the photons are coherent. There it doesn't even make sense to talk about observing 1 photon, or even a large number of discrete ones - you observe a property of the whole bunch. Even so, you can think of it as photons without too much trouble in most cases.
In fact, the insight that we observe counts is at the core of second quantization. $\mathbf{x}$ gets demoted from an observable to a parameter, to match $t$, and the field strengths become operators. It's my understanding that the field strength operators are not directly observable, but observables are built from them. Long story short, the actual observables are all built from integrating number density operators over some acceptance range of a detector.