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I'm not sure I fully understand why you need a spoof.  If you put the 301 rewrite condition in the .htaccess file, Apache will read that before doing anything else with the page, is doesn't matter if the extension will execute on Linux because it is redirected before anything happens with the actual file.

Okay; this is my opinion based advice but I'd suggest staying away from the Open Source solutions then. Some of those solutions can do great stuff, but they're so genericized to meet every potential need that there's a lot of upfront setup and config. Also the management interface is less than ideal for that number of SKUs out of the box. It's certainly doable, but you're getting into 'the custom work might cost more than buying it' territory. I've only worked with 4-5 'off the shelf' applications, but Magento sounds closest to what you want based on my experience. There might be better ones out there though. Donald Barnes raises a good point too; I directly manage and host all my e-commerce apps, so it's not an issue I've run into. But having a host who understands what your platform needs is an important step too.

Unless the bulk of your link profile is from these sites you don't stand to be negatively impacted by this.  You are just losing out on links that might have passed linkjuice before.

looks like the split testing is affecting our yahoo rankings. anyone experiencing the same issue?

Yes you should block these pages. This is a quote from Matt Cutts concerning this issue Use robots.txt to prevent crawling of search results pages or other auto-generated pages that don’t add much value for users coming from search engines Disallow: /search