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Miles,

On your last question, I'm wondering if those two canonical tags are necessary? Are the /sub/ versions of those pages necessary for user experience? If not, I'd add a canonical element to the .com version, then redirect the /sub/product.html to /product.html. That would help you avoid splitting link authority.

Yes, providing that the /category1/ and /category2/ heirarchy doesn't help the user experience (e.g. product segmentation based on say, color and brand, which would be useful for users to drill down to).

I like 301s better because they are permanent, non-ambiguous, respected by all engines, and chiefly because they eliminate the possibilty of inlink dillution because the redirected URLs are never seeen.