if you are seeing a drop in traffic over the weekend, don't panic. It's the july 4th weekend and the first week kids are out of school. People are just away from the new for a few days. Expect it to pick back up tuesday. We've seen no drop in IBLs, in fact in WMT we have seen an increase similar to the increase seen in external backlinks with the recent WMY update. Sites that have seen a drop in IBLs may have intrenal architecture issues.
If your traffic is dropping your home page PR is going to be fairly irrelevant. It's how the link equity flows from your home page to internal pages. Most sites seeing a big drop have very few links to deep pages. From what I have seen and read Google has modified how much link equity flows internally. The more clicks a page is from a page with good internal links, the worse it's going to rank.
If you were hit by mayday your best options are going to be modifying your architecture so the pages no longer ranking are "closer" to pages with good inbound links, build inbound links to deep pages, or both. If MFA sites are outranking you on some terms it's likely that they have more inbound links close to the content that's ranking and you have more links to your home page which may be several levels higher than the content you are trying to rank for.