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Depends on how good a ballhead you're talking about...something like the RRS BH-55 should be able to handle it. But you might be better off attaching the GigaPan directly to your tripod (or to a leveling base).
As everyone else said, you're going to run into light changing issues. For 120 frames right at sunset, you're going to want a shutter speed no worse than 1 second, and even that is pushing it...I'd kick up the ISO to at least 400...maybe even 800 or 1600, since you've got a 5DII...
If you wait until about 15 minutes after astronomical sunset, the light starts changing less rapidly and is still quite beautiful for cityscapes..a very deep blue if there's not too much haze or light pollution. By then, 8-10 minutes of total exposure time is probably ok.