It's really not necessary to auto generate a meta description. They have zero SEO value.

The only thing they are used for is the text that shows up in the search results. If you don't have a meta description set, Google will just pull the text from your site that it thinks it is most relevant. If you want to override that with a custom description, that's fine and can increase CTR, but this is something you would want to do manually, not auto generate it.

Link building is a necessary task, as links are still the primary factor that Google looks at when evaluating your site.

I would go for the highest PR links you think you can get. PageRank is logarithmic, which means a PR3 links is roughly 100 times higher on the PR scale than a PR2 link. It can be easier to approach smaller sites when you are just starting out, but if you have the chance at getting a PR5 link, that's worth a lot more than getting a dozen PR2s.

Interesting. Do you know if Google Analytics is installed properly? Is the code in your header? Are there any javascript errors on your page? Do you have multiple analytics scripts installed?

May be some kind of tracking issue there.

Honestly, none of these URL structures is going to have an impact on your rankings, but my preference would be for www.website.com/apples?page=2.

The more important thing is to make sure that you have your canonical tags and rel=next/prev implemented properly.

I believe Matt Cutts once said that the backlinks in GWT are updated every 3 months or so. I'm not sure if the frequency has been changed since then. I don't know how often OSE updates.

It's best to keep track of your own backlinks. As long as the page that the link is on has been indexed by Google, then it is likely already being taken into account from the algorithm's perspective.