I think you are basically asking, how do you measure velocity? First of all, the uncertainty principle involves momentum, not velocity, but since you generally know the mass of the particle, that's a minor issue. The point of the uncertainty principle is that, amazingly, even though there are many different ways to measure or infer momentum, they are all constrained by the fact that the better you know the momentum after the measurement, the more limited is your knowledge of position after the measurement.

It sounds like your question is, if I make two position measurements, can I not infer the velocity simply by noting the temporal separation between those measurements? The answer is, you could, but the result you get would not be the current velocity of the particle, after the second position measurement. Indeed, if you did that second measurement extremely accurately, the particle could next show up almost anywhere (within reason-- we don't want to consider relativistic speeds or the quantum mechanics gets a whole lot tougher). The uncertainty principle concerns what will happen next, not what has already happened.