Wow, lots of info here lol. Lets begin with the basics.
It sounds like you have had a lot of domain changes, edits, moves etc. Does Google know that your site is the "final and latest" version? Have you resubmitted the site in every available fashion (sitemap, 301 redirects, URL fetching) to Google?
Also, since you have changed to domain, any of your other authority may have been lost, especially since you state that "with all associated urls (.uk, .net, etc...) and subdomains shutdown. I've allowed all the old spammy pages (thousands of them to 404)." Some of the other sites may have had weight or authority, even if they were a bit spammy. I doubt they were being as harmful as you think, or you would have gotten a warning / penalty.
Now you are in the position of essentially starting over fresh, with little to no links, or mentions. Even if you get good "seo scores" your competitors have years of links and mentions under their belt, not to mention domain stability. Here is a starting point:
1. See if any of the old domains had domain authority or pagerank. If yes, 301 redirect to your new site.
2. Look for any pages that are indexed highly for the old domains, and 301 to the appropriate places on the new site.
3. Look at any and all social profiles connected to any of the old domains. Make sure to update to include the new URL
4. Same with directories and citations. Makes sure all display the new URL. Also look for new citations and backlink opportunities. You need to create a push of new trusted (not spammy) link to send a signal the site and URL exist.
**Also wanted to add that sometimes you can see an initial spike in rankings after launching a new site. Generally, the real results will come at arount the 30-45 day mark, once things have had time to settle, and Google has had time to fully recrawl your site.