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Well, assuming that you've already got links out to the sites that have reciprocal links back to you, removing the sites that don't will likely not improve your search engine rankings and could possibly hurt you in some areas. But like anything with SEO, it is highly subjective...one of the many variables is the quality of sites that you are linking to and how they are ranked by the search engines. Ever hear the adage "you are known by the company you keep"? The same is true of search engines. You also need to make sure that you are structured like a true directory as opposed to a link farm - you'll never get anywhere in the rankings otherwise. I haven't seen your site, just throwing it out there.
I didn't quite understand your question about a redirect script...if you can clarify it a bit I might be able to help more. Also, keep in mind that redirects and dynamic (scripted) links can negatively impact a crawler's ability to map your site.
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