I totally agree with Alan on this. You really need to look at each individual URL, and 301 redirect to ensure they are in place, page by page. It's a sensitve issue for sure and proceed with caution for sure.
It's also not condusive to 301 all URL's and links to the homepage URL. This doesn't make for a great 'user experience' and can cause confusion to the user visiting the site, looking for the specific material. It can also confuse the hell out of a search engine (where did all those other pages I had index'ed go!)
You might also damage the inbound link quality of pages in place now that have links pointing to it. Sure that would pass on to the main domain URL (losing value of 5-15% in the 301), but it's just not a great strategy tpo blindly 301 everything to the homepage. Alan said it right below - you need to look at the links, inbound anchor text, where it's coming from and redirect to the right page via 301) for the best user end experience.
I would map out all the URL's that are new, and then map out the URL's that correlate to those pages exactly. Then setup the webconfig file to have individual page level 301 redirects and put those into place. He provided a link below to his webconfig file for 301 redirects.
Cheers, Rob
Cheers.