I'd recommend engaging a forensic consultant from a reputable company. The mish-mash of advice here is mildly useful if you know what you're doing, but since you don't the only way to be somewhat confident that you're no longer compromised is to perform proper scoping and investigation.
If you've already wiped/rolled/overwritten logs then this instantly becomes more difficult. I would want to see a saved copy of your firewall configuration too, for analysis in Nipper or similar.
I'd recommend the free Redline forensic tool from Mandiant if you're unwilling to hire a consultant.