I'm very unfamiliar with it, but intuitively I would have assumed that the preferences in question wouldn't be all the preferences that the agent's value system could logically be thought to imply, but rather something like the consciously held goals at some given moment

I don't think that would be the case. The main intuitive advantage negative preference utilitarianism has over negative hedonic utilitarianism is that it considers death to be a bad thing, because it results in unsatisfied preferences. If it only counted immediate consciously held goals it might consider death a good thing, since it would prevent an agent from developing additional unsatisfied preferences in the future.

However, you are probably onto something by suggesting some method of limiting which unsatisfied preferences count as negative. "What a person is thinking about at any given moment" has the problems I pointed out earlier, but another formulation could well work better.

Otherwise total preference utilitarianism would seem to reduce to negative preference utilitarianism as well, since presumably the unsatisfied preferences would always outnumber the satisfied ones.

I believe Total Preference Utilitarianism typically avoids this by regarding the creation of at most types of unsatisfied preferences as neutral rather than negative. While there are some preferences whose dissatisfaction typically counts as negative, such as the preference not to be tortured, most preference creations are neutral. I believe that under TPU, if a person spends the majority of their life not preferring to be dead then their life is considered positive no matter how many unsatisfied preferences they have.

At least I personally find it very difficult to compare experiences of such differing magnitudes.

I feel like I could try to get some sort of ballpark by figuring how much I'm willing to pay to avoid each thing. For instance, if I had an agonizing migraine I knew would last all evening, and had a choice between paying for an instant cure pill, or a device that would magically let me avoid traffic for the next two months, I'd probably put up with the migraine.

I'd be hesitant to generalize across the whole population, however, because I've noticed that I don't seem to mind pain as much as other people, but find boredom far more frustrating than average.