I understand the logic behind blocking removing the variables. They are a lot of extra links on the page which some webmasters might prefer to manage.

What I would prefer is to reform the link so it was something like: http://noahsdad.com/treadmill-training-progress#replytocom=22729

I am guessing the "respond" portion of the URL acts as if someone pressed the reply button which seems unnecessary. If someone clicks the link whether in search results or otherwise and is taken directly to the comment, they should be quite happy. If they wish to reply they can hit the reply button.

Google ignores anything after the # character in a URL. Therefore Google would see these as simply a link to the page which should already be indexed.

Perhaps you can ask Yoast about his thoughts.

Regarding the new pages instead of posts idea, do you have a link to share?

Regarding the comment url, the page with the comment should be fully indexed either way. By changing the link, you are helping search engines better understand your site. The comment links do not represent a new page or new information.

Google clearly understands WP sites exceptionally well. I am confident you can choose various options and they will still understand those links represent comments. With that said, I would still go with Yoast on this one.

Actually, SEOmoz does it too. Take a look at their blog comments.

Is the eCommerce site Shopify SEO friendly?

It depends on how you define "SEO friendly". Have they taken some steps to improve SEO? Yes. Would I ever build a business site on that platform? No.

The nice benefits are you can get your site up and going quickly and they offer excellent hosting.

Aside from the financial expense of needing to pay monthly for the service, there are far too many limitations from any hosted solution. There are tons of SEO optimizations which are desirable but cannot be made due to you having no control over the software nor the hosting environment. Sure you can change title tags and some other changes, but that is not close to enough.

I would recommend WordPress + the eCommerce plugin or Joomla + VirtueMart over Shopify. I mention these two specifically because they offer a nice balance between a cart and a site. If you only need a cart, there are several cart solutions available.

If you do go with Shopify, be sure to get your SEOmoz discount: http://www.seomoz.org/pro-perks

Whats with the backslash in the url adding as duplicate content?

A backslash is viewed as a character. You could choose to present different content on a URL with a backslash versus without one.

mysite.com/testing does not necessarily offer the same content as mysite.com/testing/. Just because you choose to offer the same content on both pages does not mean search engines will understand your choice by default. Each URL is unique and viewed separately.

Is this a bug or something that needs to be addressed? If so, just use a redirect?

If you used the SEOmoz crawler and it notified you of an issue with some pages on your site which are viewed as duplicate content due to the addition of a backlash, it is not a bug. This issue should be addressed. A 301 redirect would likely be the best solution.

I am not clear on your question.

It sounds like your site was hacked and new web pages were added to your site. You discovered the problem and removed the added pages, thereby removing the links they created.

When you ask "Can you block backlinks from another domain", who owns the domain which have the web pages with the links? When you ask to "block" the links, block how? from whom?

My best guess is you are worried about being hacked again by the same group. It sounds like you have blocked the /data folder in robots.txt so if the same group hacked your site in the same way, the pages would not be seen or crawled by Google nor Bing since you have it blocked. If they used a new directory, that solution would not work. The best approach is to upgrade your site's security and have it tested. Change all passwords, etc.