Panthro - 7:25 pm on Jul 1, 2011 (gmt 0)
Maybe your main sites just need to out-compete your competitors' sites. You say the strategy seems to be working for the small sites, but not the two main sites. Do the two main sites cover broader topics than the network sites? If so, it's likely there is far more competition for Googlers making searches relating to those topics than the more specific topics that your smaller sites cover.
Maybe your link profile needs to be adjusted, but maybe your main sites just need to become more competitive irregardless of the link profile.