Main site PR 3 completely white hat no tricks whatsoever. Its a legitimate business site.
It was hacked for a period of one year, porn links injected due to lack of attention from my part. Haven't had time to update the theme. I was notified by google that the site was hacked then immediately uploaded the most recent clean back up i had. Cleaned a 23 Gb folder full of garbage.
Resubmitted the site and everything is fine with G verified via webmaster tools no errors no messages.
Now the problem is its not being indexed by G and some sites are still alerting that its a malicious website. PR3 is gone and the site is probably in sand box. E-articles and McAfee indicate that links are malicious as well.
Have you ever had such experience before? Whats the best method you suggest to bring it back to where it was. Again the site is purely articles and most back links are natural. Niche is very reputable, since G recognizes it as a hacked domain then clearly indicates you to resubmit it once cleaned, why would take such measures?