All Star,
This is a fantastic question. It appears you have done some homework and I will suggest a bit more along with some ideas. First, since we are an agency we face this with our clients and it is never easy. The reasons are many: Time and effort involved, cost involved (on a lot of levels), the page rank issue you describe, etc.
If I can implore you to first stop, I think you will find that preparation will be key. We have a saying here, "You do not design as you build; You design, then you build." We are clear with clients: if we do not have what we need from you to start the build from an accepted wire frame, site map, comp, content (images, text or copywriting agreement, etc.) we will not start the build. So, you have to stop all and decide one step at a time what will be there before you change. This will save you time and $$. Another thing I would say is this task is not as daunting as you may think once you get a plan in place.
I checked out your site and I must say, visually, I liked it. (I don't say that often). But, you are correct about navigation issues as I was lost quickly. So, don't change anything, yet. Go to GA and in top left you will see Audience as a left side bar first and below it, at bottom of that box, Visitor Flow. This is going to teach you where the dead ends are for sure.
My guess is you are having a lot of people bounce from the home page, when really what they need seems to be there. As you go through the Visitor Flow, you do not really need to go deeply past the 6th or 7th interaction unless you see something that seems grossly amiss. So, on first/second past go 10 or 12 interactions deep just to see what is going on and get really familiar. Then look at the pages where it seems like almost all dropped off. What were they looking for that you failed to give them? Next, look at the queries and the keywords that started all these people down the road for knowledge on what they wanted...and did not find. When you feel you have the intelligence from the data, you begin to design the changes.
I would set up a spreadsheet of dropoffs and other 'roadblocks' first. Don't get tempted to start deciding on changes yet. You have a bit to work with, but hundreds of pages is not insurmountable at all as you will see, if you stay process oriented.
As to your comment above about a grid, here is how I would approach it:
Once you know where the drop-off points are, you now will begin to design ... no, not a site map, a wire frame. Because, my suggestion is your menu structure needs changing on the home page. When I go to a page bottom menu, it takes me to the other sites. The menu structure on these is much more user friendly (with exception of top right two items) IMO. With designing the wire frame you want to keep this home page fairly close, but IMO the bottom menu should be right or left. If you are losing anyone from top menu, I think there may be a different issue than architecture. You may need a bit more info/direction for those going to top items. (In lead gen with this vertical I am unsure as sometimes, less is more. If you like your results here - do not change it at all). NOTE: Given you have essentially 'two' sites in structure, you may want to look at two wire frames. One for home/landing site and top level items - one for bottom menu items.
Once you know your wire frame, then you begin the site map (your grid essentially). Use what you have learned to determine where the changes should be, but follow the common rules of get them there in steps of three (or four if must be) clicks max. And, here is a good answer around ecommerce sites from Alan Bleiweiss around url structure for ecommerce that I think is applicable - look at his explanation along with the structure for the pearls.
Because of the way you have set up the individual sites you will have an opportunity to self correct a bit. You can take one of the mid traffic sites from the bottom menu and use it as a guinea pig of sorts. (I understand in some ways it will link out to dead ends you haven't changed, but it still could provide clues going forward). Don't be tempted to go with the worst as it might not give enough data.
Once you have processed the data from this, you can reassess your site map, make needed changes, and prepare to launch remake. Stay with it, do not rush. Your enemy will be trying to, "get it done." I promise if you do the research and plan the design before you start, you will get it done really quickly once you commence.
The devil is in the preparation. Make sure you remember to 301 in .htaccess file all changed urls so that the link juice passes to new url. Also, resubmit site map when you finish so that you are sure Google is aware and reindexes asap.
Lastly, on the whole, this is a nice site IMO. You still need to get the on page corrected: duped meta descriptions mean you do not answer the query in the search snippet. Think about it, how many clicks are you losing? Have someone that can take simple direction go through and take out all the keywords from your CMS. You have title tags that are longer than your urls and do not help you.
The beauty is in your clean look and your content that is not a bunch of duplicated, stolen, spun, BS. I do applaud that for a site like this.
Thanks for giving me a little fun this morning,
Good Luck and I hope to see results in a month or two!
Robert
PS: Please do not design as you build; design it all, then build it.