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What you should see is search engines delivering people directly to your product page instead of landing them on your interstitial category page, which should help you out. In general, the less pages a potential customer has to navigate to get to the product that they are looking for, the more likely they will purchase it.
Jon,
If there is no content and these pages are just the download link then instead of putting a canonical link on them, set them as noindex. I assume you have a landing page that directs people to your downloads, this is where you should optimize your content to get organic traffic, the direct download pages (with 0 content) will have no real value from a search perspective.
While it is possible, it is not easy to set up nor would i recommend it. If you are having issues to the level that you are considering using GTM as your CMS, it is time to invest in a proper CMS for your website.
Make sure you have all of your new urls plotted and are ready to implement 301 redirects for each one. Also make sure to go back and update your current 301s so that they are pointing to the newest pages, not creating chains of redirects.
Also, don't be surprised if you take a small hit from moving many of those pages further from your root directory, as long as your content is relevant you should be able to bounce back within 90 or so days, but expect drops even with full 301 redirects.
Set up Canonical tags and use Google's UTM codes to track your non-internal links (as your internal links will be tracked just fine by Google Analytics without any need for using redirects).
You should find the locations of those links and correct them to point to the proper URL. I find that Screaming Frog's crawl is the easiest for this, you can find every link and see where they are located.
Kirk, 301s are the correct choice, and there is nothing wrong with having multiple 301s point to a url, it is very common. IF you are doing a full set of new urls, make sure you go back to any old 301 redirects and point them directly at active pages, you will lose out if you are creating long 301 chains.
You are correct, the more user readable friendly (short, easy to understand, without long alpha-numeric strings) your urls are the better they should perform, as long as your on page content is considered relevant by Google for whatever terms it is using.
Google is all about serving the best experience with the best content. When you put tabbed content on a website, especially if the tabs serve multiple topics, you are watering down that page. Also because a portion of the content starts at hidden, it makes a worse UX experience for a user to directly get to your content (because they have to click).