There appears to be a fundamental issue with the eay your search results link to your products.

Is this store based on Cubecart. I had a similar issue a while ago whith CC and I managed to fix it by changing the code on the search results page to build the full path to the product rather than the shorter URL without the category folders.

One way would be to ensure that products carry a canonical tag pointing to the actual page URL?

Checkout the guide below to Canonical Tags.

http://www.seomoz.org/blog/canonical-url-tag-the-most-important-advancement-in-seo-practices-since-sitemaps

Though I would recommend fixing the issue at the root and modifying the way the search links to products.

I don't think so, however I have written my own link management software that on acquisition adds an enty into a database then its crawled regularly to determine the links status. This gives me a supposed acquirement date.

Ive run your site through the Page Speed tool here and you get 94/100 (which is awesome!).

No idea on the JS sorry

I'd be more than happy with 94/100!

From a usability perspective I'd look at the redirects as a 404 is some what off putting when your trying to buy. It could lead to visitors losing trust and ultimately sales.

In turn, if usbility is effected in such a way then doubtless the SEO will follow.

If you have matching products which have indexed pages with some page authority, then I'd take the time to redirect them.

Your compromise is not bad, it would save a mountain of time which can be devoted to other cool things and its certainly better than several thousand 404 errors!