Motion Capture Project - Tracking Fluids

I have several objectives for this project. The main motivation is to motion track some "particles" in fluids and then use this as a way to reconstruct the fluid mechanics, interactions etc. I want to start off with a simple "2d" simulation device. I think I could build this pretty easily (hopefully cheaply) and just track objects falling in some liquid (probably water at first, but I'll have to see as I go for viscosity reasons). I could then try to simulate some sort of 2d cavity flow (see below) with a pump/hose. One of my big issues, clearly is where to put this, but I'll have to see as I go.

Once I have this working, tracking my "particles" in 2d with one camera, I can start thinking more about 3d. THere are many questions here, obviously, including how many cameras (or mirrors) do I need, do I want to bother with underwater cameras now (doubtful - $$), what algorithms to use for the 3d reconstruction, etc.

I would like to get my 2d setup built and running in a month and start tracking (I'll have to figure out best tracking system since I want rotations obviously). After that, I would like to start working on the 3d setup. Most likely, I won't get too far, but getting the setup and running and figuring out how many cameras I need would be ideal.

Below are some preliminary sketches I made:

Some links to motivations, help, etc:
Dan R suggested Rheoscopic fluids may help - potentially:
Ron Fedkiw - nice 3d simulations
Work I did with George Biros, Lexing Ying and Denis Zorin - simulating their solver
NYU's App. Math Lab - good place to go to ask Mike Shelley questions if I have any on construction and implementation

Diary - Unanswered Questions
3d reconstruction of mocap data?
best tracking algorithms to use?
More questions will be put here and below - I want to use this space to talk to myself and add info.