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First of all, you should try and visit the website using Google Webmaster Tools (with the 'visit as Google Bot' tool). If it shows a HTTP 301 redirect to the .com website, you'll know everything is working fine but your site just hasn't been indexed yet since the change.

If it shows anything else (probably the holding page), there might be something wrong with the way you redirect. You can try using one of the plugins to check for HTTP statuses (FireBug and Chrome's developer tools have basic features, FireFox's Live HTTP Headers plugin can show you more). See what is says the HTTP status is, and try and fix it.

If that were true, it would be possible to take out a competitor by setting up a link campaign to their website. I do not believe Google would allow such a thing to happen, so while I'm not 100% certain I think it's safe to say bad inlinks will not harm you. I must admit though, the two observations (dropping search engine traffic and a huge amount of bad inlinks) do seem rather coincidental, especially taking in account that the Panda update hit in February.