Well, you own a ccTLD for India. So Google will see it as primarily for India. That's, more or less, the purpose of ccTLDs. It doesn't surprise me that WMT won't let you remove that hinting.

Now, does that mean you can only rank well for India? Absolutely not! You can still rank well for US rankings. Something more powerful than your ccTLD is the power of relevant links from US sources. Get some links from US sites and Google will start seeing you as relevant for US searches. I see that happen all the time with UK sites.

It's not related to Gmail. The server itself was sending out email spam (Joomla is a CMS program used to manage websites). I bet he means he got listed on Spamhaus.

First off, web spam and email spam are two entirely separate things. So you can be blacklisted with anyone in the email realm and not have it affect your SEO.

Second, I've heard the "blacklisted IP" theory regurgitated for nearly 10 years now and nobody has ever proven that a specific IP was the reason for a site losing ranking. So you could, in theory, share an IP with an entire link farm and not lose any ranking (consider how many blogs share an IP under Wordpress.com or Blogspot). Google surfs the web just like everyone else (using DNS lookups) and they rank domains, not IPs (which are subject to change). The only way I could see an IP getting you in trouble is if your server got hacked and the hacker was using it to proxy attacks against Google (as in DDoS attacks, not spam). Then you might have some issues with SEO but your server being hacked would be a far more serious problem at that point.

Google is not going to render the animations, nor your loading image. So in terms of spidering, that shouldn't be a big deal.

The site seemed to be relatively fast in loading but I noticed you're not using a CDN to load all that extra content. I would highly recommend moving all that off to something like Amazon CloudFront. That should help your load times some.

Your site uses HTML5 so you might want to look into asynchronously loading some of your scripts. I noticed in Firebug that several scripts spent a long time being blocked (notably some Google scripts I didn't recognize)

Does it still resolve to your site? If not, it should fall off as Google spiders it again.

Your htaccess file can do the 301 (it's actually a config file you can control). Here's some sample code that should do the trick.

RewriteEngine on
RewriteCond %{HTTP_HOST} .
RewriteCond %{HTTP_HOST} !^www.domain.com
RewriteRule (.*) http://www.domain.com/$1 [R=301,L]

That sounds like a bad web server config. Most servers run a virtual host, meaning the URL determines what website is served up. Either you have your own virtual dedicated server and only one site that isn't using vhost, or your host has set your website up as the default site.

If you have control over the web server config, I would add the malicious site to the config as a hosted site and then have it return a 404. That should de-index it.

If you don't have that level of control, try to get a 301 redirect for the bad domain. You really need  something like an htaccess that says if a site is accessing my website as anything but www.mydomain.com it needs to 301 to that URL. Otherwise anyone in the world can hijack your site the way it's set up now. Just point another A record and instant duplicate content headaches.