Hmm, I'm confused, you want to change shorts 2 times for a sprint? Or are your running shorts the same as your compression shorts? If the running shorts are the same as your compression shorts, then your plan sounds good. If not, I would imagine it would be hard to swim in running shorts, and you won't have a place to change, other than in transition, and *ahem* exposure is generally not allowed.

As far as making up for the missed workouts, its probably not necessary. 3 days is not too much to worry about. I would stick with your original plan, do what you have done if you hadn't gotten sick. That's just my opinion, someone else wiser than me may have better advice. Good luck, and be sure to come back and tell us how it went!