So sorry for the delay getting back to you, its been a crazy week and didnt notice the response.
"Note that this is a manual penalty though, so fortunately no waiting for Penguin refreshes."
OK, just to let you know, once they lift the manual penalty, you still need to wait for a Penguin refresh. my penalty was lifted in May 2013 the vast majority of crap links had not been crawled and took a very long time for Google to do so. For the disavow file to take effect it needs to crawl each of those pages with your disavow file in mind and change them to a nofollow. Once a healthy amount is crawled you will then be in good standing when the Penguin algo is run. If Penguin runs before you have an acceptable level of healthiness you will not be released form Penguin and will have to wait for the next. So it took us until Oct 17th 2014 for us to finally get released. This was WITH John Muellers help!
My advice is don't be too picky with what you keep. Go through everything, mine was 20,000 Referring domains with 250k links! We had a 10 year history of business online and at one point also attacked with negative seo. So was a big job
"Providing I've given all possible evidence I can about the links being live or not to Google, do you think that disavowing all poor quality links that APPEAR to be no longer live is good enough in Google's eyes? Obviously for all links that are still live (as far as i can see) I have outreached to at least 3 times and disavowed if I can't get in touch."
Yes, create a report to show the work you have done, whats removed, who you have contacted, who did not respond. I did an Excel spreadsheet, one domain per line, with a few fields like, last contacted, date, removed etc..
There are lots of programmes out there that help with this now. Not so easy when your the first and there are no tools for it!
Also its best to do domain instead of links, how many links do you have pointing to your site?