Hi there,
Complete your 301 redirects, but do it 1-on-1 basis - one old URL toward one new URL. DO NOT redirect all your URLs to your home page. (after you do that, verify to make sure is indeed 301 redirect and not other types of redirects like 302).
a) The most beneficial way is to 301 redirect as much as possible following a structural way: the old categories to the new categories and so on. Don't worry there are no limits on how many 301 redirects you can use, just don't loop them with intermediary redirects, like: old URL -> 301 -> intermediary URL -> 301 -> final active URL. Go directly from the old to the new, final, active URL in 1 step if possible.
b) Verify if in your Webmaster Tools there are old Sitemaps. If there are, delete the old ones and create new ones that have to contain only new URLs.
c) Make the same move for the robots.txt file as well. (If you don't have a robots.txt file, create one and place it in the root of your domain name, e.g. www.example.com/robots.txt )
d) If possible, use all instances of "fetch as google bot" and then subscribe those URLs for crawling but do it as much as possible for the main node pages from your website (e.g. main categories), don't waste this function for final product pages, as Googlebot will go link-by-link from the categories and will re-discover all your URLs.
e) Be patient, the Page Rank and old traffic flow won't happen over night. It can take up to 3 months for Googlebot to re-discover and re-index all the pages of your website (i know it's a long time but usually happens a lot sooner).
f) Keep a close eye on Webmaster Tools account and make sure you solve any problems that appear in a due time.
g) Scan your entire new website with a software to make sure you don't have broken links, it's important. If you find any broken links, solve them imediately.
I hope it helps.
