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Can you share the listing? I can provide some feedback with the NAP. Also, did it used to rank?

Are you able to share the domain name? This can at least give us some more insight as to what may have occurred.

Bob,

Thanks for the feedback! I hope you find great success in local SEO! One side note is that services like Yext will submit 40+ instantaneously with no harmful effects. That's just an interesting data point since if you're doing them by hand there's no way you could ever do that In the same amount of time!

Yes, building citations is not the most exciting task in the world. However a lot of times you will see the added benefit of gaining new customers through the other sites where your business is listed. Good luck and keep the data consistent.

The new NAP is actually NAP+W (W meaning website). That's what they're teaching at local U Advanced and I agree.  Basically wherever you have a citation you should try to get a link. Everywhere you have a link you can also try to get a citation.

Many citation sources will give you a no follow link but having a mixture of follow and no follow links is natural and good. When you add these citations it may take a while for them to get indexed too. Many of these directories are huge and put your listing deep within them. Long story short... If you are building citations manually (even using the Roboform method in my Moz Post to speed it up) you should have nothing to worry about.

You will be surprised to see how long some citations take to get indexed and then how long they will take to help you. Don't forget to submit your listing to the major data aggregates like Axciom, Localeze, Infogroup etc.

Are these local locations in each of the areas? You will want a local phone number for each business location if you want to be the best in Google's eyes. Using one phone number with multiple addresses will create data confusion in Google's eyes and can adversely affect your Google Plus Local rankings.  You can then add your 800 number to each location as a secondary phone number.

In a nutshell using one phone number is a bad idea.

You can set the preferred domain just like Geoff mentioned. But basically since you have a www version and a non www version it can be seen as duplicate content. Although the site is only one website and changes will appear on each the URL structure changes for depending on if you use the www or non www and therefore it looks like duplicate content.