I use the following tools:

1. Xenu - identifies broken links
2. GSite Enterprise Crawler - identifies on page issues
3. Google Cache, Google Webmaster Tools - finds crawling issues
4. Scritch - finds server/platform type
5. Ahrefs, Majestic, OSE - for link diagnostics
6. SEO Book Bulk Server Header Tool

I haven't seen a .io in the English SERPs as well, why not register a .io and see if you can get it to rank. The test should take less than a month and if it ranks then you can consider redirecting it to your .io domain.

If you focus on brand building, then yes, you'll offset any losses. The EMD will pick out poor quality EMDs without the requisite quality content.

Also, the loss from the 301 is not a short term loss, it's a permanent loss.

I would recommend leaving it as it is because despite the general consensus about 301 redirects transferring all link equity and traffic, the truth of the matter is that you will experience a small permanent loss in traffic every time a 301 redirect is utilized.

I would simply not take that risk as there are many things that can go wrong.

To make sure that I'm getting your question correct. You want Google to crawl and index all your content but you want visitors to use an open paywall that shows 5 free articles then resorts to a paywall.

Yes, it would be treated as cloaking but you have a legitimate reason for doing so and intent matters a great deal. You could check for a search engine user-agent string such as  "Googlebot" and then serve the full content. This would ensure that your content is still crawled and indexed.

The only downside is any tech savvy individual can spoof the server header by setting their user-agent to "Googlebot" and bypass your paywall.