Domain hacked and redirected to another domain

[Dantek]

2 weeks ago my home page plus some others had a 301 redirect to another cloned domain for about 1 week (due to a hack).The original pages were then de-indexed and the new bad domain was indexed and in effect stole my rankings.Then the 301 was removed/cleaned from my domain and the bad domain was fully de-indexed via a request I made in WMT (this was 1 week ago).Then my pages came back into the index but without any ranking power (as if it's just in the supplemental index).It's been like this for a week now and the algorithms have not been able to correct it. So how do I get this damage undone or corrected?  Can someone at Google reverse/cancel the 301 ranking transfer since the algorithms don't seem to be able to?I have the option to do a "Change of Address" in WMT from bad domain to my domain.  But I don't think this would work properly because it says I also need to place a 301 on the bad domain back to mine. Would a change of address still work without the 301?Please advise/help what to do in order to get my rankings back to where they were.

[Atlanta-SMO]

Has your .htaccess file been modified at all?

[Dantek]

No, a backdoor was planted and then some joomla files and wordpress files (another site on same server) were modified with additional base64 encoded code that instructed with a 301 redirect if the agent was not a browser. So basically all search bots were getting a 301.

[Dantek]

Oh wow....it's back!!!  For over a week I've been stressing with this and the lost traffic/sales.

Yeehaw  I can now enjoy my weekend.   Although I still have some forensics to focus on but still, a big relief.