I don't know how helpful this will be but we have recently been quite successful with a similar approach for one of our clients.
When their site was launched it was enjoying good rankings for their core categories and great conversions. Over time a ton of content was added all over the place and the homepage looked like a Xmas tree with the links, baubles and buttons on it. After about a year they started to slip and revenue on the core categories was dropping like a lead canary.
We got called in, asked them to be brutally honest about the importance of each category and created a hierarchy for them to sign off on. Once we had that we removed the non-critical links from both the homepage and the main nav, relegating them to sub-menus. We also cleaned up a whole bunch of other stuff that really should have been caught earlier.
The end result was an average 35% increase in conversions on the core categories within a month. Interestingly the "secondary" categories I thought we were possible sacrificing didn't suffer at all - most also saw modest increases.
Check Richard Baxter's posts - he is brilliant at this sort of thing and I'm sure he had something recently on choosing your homepage links in one of his presentations. You might be better off stepping back and following his approach from scratch to see what really needs to be there.
Hope this is of some help.