Frank, you made a good observation about the similarities between traditional qualia and the flow of time. As I understand it, anything that we experience has all of the necessary properties of a quale. Since we experience the flow of time, surely we can find things that are similar in this experience to other quale, surely with it the problems that come up in discussions of other quale.
Before I look into other similarities, let's first look at traditional quale, like color or taste. When I talk about the flavor of onions, it's difficult, maybe even impossible (for now, at least), to determine if that sensation is exactly the same as yours. And when I say blue, perhaps you're actually thinking of what I think of as red. As of yet, science hasn't given us the tools to compare these things. Personally, I think of this as the property of qualia that give them any weight, or philosophical meaning.
If we could compare color, then who would about the quale of color, then, right? Sure, they'd still be experience just the same, but when I hear qualia I immediately think of the subjective, incomparable nature of experience. If we could compare things, calling them qualia would seem inappropriate. I almost define qualia as our experience that we can't compare. If we take this definition, then the ability to compare colors would exclude them from the class of things that are qualia.
Anyway, back to time. When we the experience of time, it seems the only properties we could disagree on are the direction of flow and the rate of flow. Physics (in particular, thermodynamics and its irreversible processes) gives us reasons to think that time couldn't flow backwards. If you accept this as true (I don't think you need to, but you might be persuaded by physics), then you can only talk about the rate of flow. Could we disagree on the rate of flow? I think so. Perhaps what feels like an hour to me feels like a minute (how I experience it) to you.
Allow me to take a break for a moment to discuss cause and effect. In the simplest form, cause and effect says nothing about rate of processes occurring. It refers solely to the direction of time flow. Accordingly, if you happen to be persuaded by physics that we physically could not experience time in the other way, then it seems that cause and effect loses that fundamental of quale: the inability to compare. If everyone experiences time in the same direction, and we know this, then who cares? It'd be like being able to compare colors above.
Anyway, back to the flow of time. Up until now, there seems to be no reason to distinguish the experience of the flow of time from other qualia. But I'm wondering if it'd be possible for us to determine the rate of flow for an individual? Perhaps from something like brain waves or properties of your neurons? Might there be something which we can now observe that would lead us to think that someone is actually experiencing time faster.
An example I'm thinking about would be someone who has faster reflexes than someone else. Now, there are at least two types of examples that could lead someone to have faster reflexes. The first is that they have simply have more neural connectivity that allows this person to perform a given activity faster. The other possibility would be two people who have identical neural structures, yet one is lacking myelin sheaths. Instances of the second sort seem more important to this discussion. In the first case, the electrons in the brain are traveling at the same speed, they just have further to go. In the second case, the electrons actually are moving slower.
But the question remains as to whether or not we would experience time slower if the electrons in our brain were going slower. I'd like to think that it would. We have reason to believe that all our experiential processing happens in our brain, so surely if our brain was processing things slower that would lead to a sluggish experience of time? This hinges on electrons being the mediating particle in brain processing, which I'm not sure we have any strong reason to believe. But it seems possible.
Maybe you disagree or are unconvinced. That is completely fine. I'm just writing some thoughts I found interesting and relevant to your question. I hope you at least find them interesting, if not convincing. =)