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1) Sorry, not sure about this, but you may want to reconfigure your site to have SE-friendly URLs (no query strings). This has the added benefit of being able to put your keywords in your URLs.
2) I don't believe this is directly possible. But if you use mod_rewrite, you can make your pages in each store look like they're under different directories, which GA can track separately.
For example,
/store33105/product123
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