Untrusted site - malware!

[Llanero]

I recently had my link profile done as I was badly effected by something in 2012 (Penguin, Panda.. who knows? never got a message from google in webmaster about anything).

Loads of INBOUND links were identified as being 'dodgy'' and the person highlighted them in different colors. However, another seo éxpert' told me to leave them (perhaps remove just 3 of them) and don't bother with the rest. Now I am not sure what to do? Any opinions?

RED
3 were highlighted as being from untrusted malware. I think I should disavow them but really, would 3 make that much difference for a fall in my site?

ORANGE
240 were said to be spam articles and I was advised:
The following pages highlighted in orange are on sites created for the purpose of publishing articles for link building. Since the same articles appear on multiple sites, Google views this as duplicate content. Links to Monteverde Tours in these articles should be removed or tagged "nofollow." Where this is not possible, the domains should be disavowed.

YELLOW
85 were said to be from Low-quality directories
The following pages highlighted in yellow are on low-quality directories and link farms. Links to Monteverde Tours on these pages should be removed or the domains disavowed.

GREEN
340 were said to be from sites were the page was not found , Account suspended, Problem loading page, Link removed, domain expired
The following pages highlighted in green include pages whose links to Monteverde Tours have been removed and pages that were inaccessible for various reasons, as shown in the Comments column. These pages or their domains should be disavowed to remove them from the Google index.

I have read (and asked on this forum) about disavow but the more I read the more I am getting confused about the next action. I tried for one year to get rid of any bad outbound links, did blogging, social media, improved content, landing pages etc but all to no avail.

Any opinions appreciated. I am not looking for a magic bullet, I know there isn't one. I know I need to keep improving content etc  but after a year of NO improvements should I consider the link removal route?

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| Untrusted site - malware! |

[Highland]

These pages or their domains should be disavowed to remove them from the Google index.

The disavow tool can't affect whether or not your site is indexed (or I could disavow all my competitors). Disavow is a hint to Google that tells Google "Please don't count this link towards page rank". In other words, disavow, more or less, lets you reach into another person's site and nofollow the link to you.

So, should you use it? Unless you have WMT messages telling you you have a manual penalty, don't touch it. Most likely the links in question are already devalued. If you use it, you could disavow links actually helping you and thus do yourself harm.

MALWARE!!!!

Unless there's malware on your site, links from sites that have malware on them won't hurt you (simply because they have malware)