Hmmm....
The Gigapan always struck me as offering a battery powered solution to a non-existent problem.... but anyway. If I was using one, it would be with a moderately long, ultra-low distortion lens (in other words, probably a macro lens.) From reviews I've read, the Gigapan has a very limited carrying capacity, so take this into account.
With any TS-E (I also use the 17) you should move the camera from side-to-side rather than moving the lens. This avoids issues with changing your viewpoint. It's probably significant for subjects that are within a couple of feet of the lens.
The easy way to do this is mount your camera on a macro rail (or something similar.) Moving the lens through it's full travel should require about 24 mm of motion. Occasionally, I will move the lens along the 30degree and 150degree orientations (requires 4 frames instead of 2 but you end up with a frame thats more conventionally shaped.) If you do this, you need to displace the camera 10.4mm left and right but also 6mm up and down. It can become a little trying.
Ok... now getting more coverage on panoramas...
I don't think the 17 TS-E is the ideal lens for this because it stretches the image in the corners of the frame. This is unavoidable in a rectilinear lens design. If you really need to go wider than the TSE offers, consider mounting a 50mm lens on the camera and shoot images in portrait orientation. The ZE 2/50 MP offers less than 1% distortion, so maybe that's worth considering. If you want to get the very best results, the camera / lens system needs to spin about the lens' nodal point. You could do that with the same rail I referred to above.