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After reviewing pisoftware.com, you only need https for the Login/Signup page. Why the hell would you need https for other web-pages as they are only "informational" pages; there's no transactions or sensitive information on them.
Putting the entire site in https is just a bad idea.
As per your Italian Restaurant example, the best links will be from other Italian Restaurant websites.
The million dollar questions is, how do you get your competitors to link back to you? Why would they do that and benefits would they get from it?
If your websites link extensively to each other thus forming a "Private SEO Linking Network", then yes, having it all together on one Server or Data Center is a bad thing.
However, just because each website has its own hosting plan with Go Daddy doesn't mean that they are on different Servers or Data Centers. Odds are, they are all probably in the same Data Center anyway (physically located in the same place).
Chances are, moving to an "Ultimate Hosting Plan" will not result in any changes to your websites; it will just be an "Accounting" change.
What you are describing is not a shopping cart website; it sounds more like a "classified" website. Maybe the WP plugin below is suitable? I haven't tried it myself by it seems to have all the features that you need.
http://wordpress.org/plugins/another-wordpress-classifieds-plugin/
How much did your client's site go down? It could be just from natural fluctuations or SEO work from competitors.
Duplicate Meta Description Tags are not a factor in search engine rankings.
The main purpose of Meta Description Tags is to be used as a sales pitch with a call-to-action to entice the user to click on your search result. There's no reason why you can't be a bit creative and vary your sales pitch a bit.
Your Home Page is http://www.bannerbuzz.com/ while your Reviews are on http://reviews.bannerbuzz.com/review/18/Vinyl-Banners.
The first problem is that your Home Page is on the "www" subdomain while your Review Page is on the "reviews" subdomain. Subdomains are treated as separate websites by Google and so they are basically competing against each other for the same keywords.
I recommend moving your reviews to a sub-directory under the www subdomain so that your Reviews will have the URL like the following: http://www.bannerbuzz.com/reviews/18/Vinyl-Banners/
Your Review page has a lot more Text content than your Home Page. If you want to boost the rankings for your Home Page, make sure to increase its Text content.
Also, since you sell different types of banners, I reckon the Home Page shouldn't be the Landing Page for "vinyl banners". You should use one of your Vinyl Banner Category Pages instead:
With Open Site Explorer, I compared your web-page with 4 randomly selected competitors from Page 1 of Google. Results are here:
https://www.diigo.com/item/image/4380n/pk93?size=o
From the results, it's obvious that your Page Authority and Domain Authority are lower than your competitors. You just need more good quality external followed back-links from good quality, trusted websites.
You can use the 'rel = "canonical" tag' on your microsite to specify that "coolprograms.nonprofit-mainsite.org" is the preferred domain for indexing.
http://support.google.com/webmasters/bin/answer.py?hl=en&answer=139394
You stated that you publish infographics with an embed code carrying anchor text pointing to your Home Page. Why don't you change that so that it points to your various Landing Pages?
Alternatively, you can publish the infographic on your targeted Landing Page and advertise the fact on your blog post with a link to the Landing Page from the blog post.