ya, I just did a whole bunch of this kind of thing…
What you are looking for is shape keys. They are located on the other tab with the modifiers in 2.49.
To use them just add one shape key without moving anything.
That is you basis, so don’t touch it again just create it then tab in and out of edit mode so it sticks.
Then create another on while in object mode.
Then go into edit mode and move vertices around, and go back to object mode.
When you are in object mode you will see a slider in the shape keys box if you move it, you will see your mesh move.
So to make this easier just divide a window so that you have an actions window and hit zero so that you are looking through the camera. Make sure that the video is in the background and that your camera frame and lens are set up properly or your going to pay for it by having to redo everything later.
Go ahead and create a shape key. Normally I will put the frame number into the shape key name box so that they are easier to find and adjust later.
So then go for it. move your timeline forward until the shape of the thing you are masking is at an apex. That is the shape has moved all the way in one direction and is about to move in another. At that point add a shape key. If you have an actions window open you can go to the view menu in it and click “show sliders” Then you want to have three keys for each position. The last one off. The current one on. The next one off. If you forget to turn off the keys in each new position you mesh will look all screwy so don’t forget that.
If you need help setting up nodes for blending your matte let me know…