I'm not a mold remediation guy, but I'm a homeowner have dealt a little bit with this. I'm assuming traditional stick built home. Here's what I would do:
1. Get your roof issue fixed. If this is causing water intrusion into the house, you've got to get this fixed immediately.
2. Get the area inspected that experienced moisture. Any competent person (including yourself) should be able to visually identify rafters/joists that have mold, mildew, or rot. Anything with rot needs to be replaced. Anything with surface mold or mildew should just be able to be sprayed and wiped down with bleach water.
3. I would think that once the two above items have been completed, the smell should go away pretty quickly. However, if it's that strong in the house, it may be more widespread than just your attic (another assumption that water damage is primarily in your attic). Your home's HVAC should be pretty much sealed off from the attic.
Again, not professional advice, just some thoughts having been in a somewhat similar situation with mold/mildew in our home HVAC system.