I checked a site in Website Insight and saw that scripts account for 69% of the index page weight. The site has a CC menu on it and already had some scripts.
Does it matter that there are 2 versions of Modernizr and 2 versions of Jquery on each page?

You should be able to dump one version depending on which each is doing. Some scripts are backward compatible and some are only compatible from one version forward or from one version back. Commenting out is an easy way to test the necessity of each version. You may need to adjust the scripts if their customized to bind to a particular element.

I have jquery-1.10.1.min.js on the site, the menu uses jquery-1.8.2.min.js. I guess I'll see what happens without the older version on there.
Does it matter if the Jquery script link is at the bottom of the page, rather than with the menu script links in the header?

It's recommended to place scripts at the bottom of the page but it's not always possible. I do both depending on how the site loads. Some sliders will load better if the scripts are in the head of the page. Scripts that reference other hosts will typically go at the bottom of the page because of the possibility of a slow server.

I usually have Modernizr at top and the others at the bottom. I haven't tried splitting up the CC MB stuff – leaving the CSS at the top and moving the JS to the bottom. Is it best for MB to leave all those together in the head section?
I'm thinking I should copy the site and do some experimenting.

That's what I recommend. It may make a difference but it may not be enough to even notice.