You definitely need the 301 from www to non-www or vice versa.
As to the rest, the damage is done, and the key to the changes suggested above is that they remove hindrance - and help a little - to get the site re-indexed.
When you change things to the extent that you have, then the risk is that Google effectively sees a new site, and treats it accordingly. So you now need a 'clean' site to avoid the 'sandbox'-type purgatory for a few months.
The site map - and a Google site map - will definitely help, as will clearing up the Google verification confusion.
I agree that you need to be very careful with reciprocal links - any to non-related, and/or non-quality sites should go. Now.
Also, xenu is your friend - do check it out!
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