Thank you for the response. I ended up disabling pagination on the category pages (as there aren't more than 20-30 posts per category) to fix the duplicate content issues caused by paginating each page 5-10 times with the same 1000 word article on each page.
I then fixed the author page Titles and Description issue by adding some dynamic tags provided by Yoast in the Author page. Simply changing it from "All Posts by (Author) - Site Name" to "All Posts by (Author) - Page 2 of 36 - Site Name" dynamically, it fixed the duplicate titles completely. Same with the meta description..
As for the home page links, I changed the linking structure entirely. Instead of random posts per category, it now has a link to each category page with the 5 most recently added articles per category under them with a link, image, and text snippet so the page will be more "static" for a while and provide some link flow to my new content, but still update as i add content. I then moved the top 5 posts of all time in the sidebar followed by the most trending article from the last 7 days (by view count).
Finally, I customized my 404 page to show the top 3 articles from my top 3 categories after reading an article about keeping your 404 page relevant and helpful to your viewers just in case I have a bad link come in.
I made all of these changes about a week ago and am waiting to see any changes in rankings, but I think, at least from a reader's viewpoint, the site looks much cleaner and easier to navigate. It didn't make a whole lot of sense to just randomly display whatever the theme felt like every refresh.
Thanks again!