Thanks for the input Kronomia. Perhaps I should have described a little more about the nature of the web site to give you some context.
The site is a personal web site, containing a number of articles I wrote on the subject of health. It is not a commercial web site. The only income generation on it is Adsense. I have been tracking my visitor stats since the site's inception in 2006. The unique visits peaked around 2009 or 2010 and slowly trailed off. It is hard to prove that it has anything to do with either Panda or Penguin, and could very well just be an organic decrease in visits, because other sites and blogs have become more interesting or visitors are more demanding regarding web site formatting etc. I did however notice a marked drop in traffic in the month or so following Panda. Traffic continued to drop and is now less than 25% of what it was. The revenue from Adsense in that time has dropped, and whilst it fluctuates, is maybe 25% or less of what it was.
I do have another personal web site, one which has never had any issues with bad backlinks as far as I'm aware (there are very few backlinks of any kind!) but it has had the above formatting issues as described in 1 to 5 in the OP. The traffic on that site has dropped to 30-50% of what it was over the same time period. So not hit quite as badly as the health site which the OP was about but still highly significant. I also noticed that my page ranking for that site on certain word searches on google was not as good as it once was, perhaps due to increased competition from others site, but perhaps for the above reasons 1 to 5.
Kiwiheretic - thanks for raising a good point. I did notice surges in visits on my site on occasion, but it tends to be a brief peak. Of course, I can't guarantee that it isn't as you have said above, but the drop in revenues do suggest that it is related to a real drop in human visitors.
I have never engaged in the practice of spamming links on other sites. Sure, I've put a link in a comment or blog on occasion, but generally when it was relevant or where I contributed to the discussion on the blog. No more than half a dozen times perhaps. I used my web site URL in my signature on a few recreational forums for a while and have since removed the URL from the signature. The posts on most of these forums have been updated accordingly but at least one still has my URL in my old posts (non-relevant links). Not sure if this would be penalising me or not. I put my URL in the description of an ebay auction also to provide more information on a given subject, and tend to host images on my site for ebay auctions (as I've already paid for the hosting). I suspect the forum signature may be hurting my web site? It only just struck me as I was writing this that it might be.
When you say 1) move to a new site, do you mean ditch the domain name completely and use another one, starting with a clean sheet? I have an alternative domain name I could use. I paid a lot of money for it. My existing domain name wasn't cheap either, so I wouldn't simply 'drop' it, I'd want to sell it, and if I did, I'd want to clear up any bad backlinks (if at all) as they would reduce the sale price. The domainer would sold it to me in 2011 evidently wasn't aware of the backlinks or kept quiet about it. My current domain name is punchy but perhaps not ideal as it has the word 'medical' in it.
I would never hire a professional developer - if it was a business site then yes I would consider it, but not for a personal or non-profit web site with around 200 unique visits a day. My coding and SEO skills are hugely better than they were when I first started. I may reformat the site slightly in any case.
3 - yes this is true - if I do rewrite or chop up the site I will certainly lean towards this mentality. If I do rewrite it, I want it to be something unique, with an unique attraction for visitors.
4 - granted, I think I know most of the techniques now.
5 - this would be a nice to have, but it wouldn't make sense for me to spend too much time on generating high quality backlinks for a small, non-profit site. I have a business web site I run which has none of the above problems and my focus as far as proactive marketing is on that.
You are right that I should focus on the cure, not the problems. I was just phrasing my initial post in terms of what potentially might be afflicting it, but when it comes to rewriting sections or planning for a new format, I focus on the glass being half full and what would make a good web site.