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A little while back a whole heap (around 5000) of exact match anchor text links showed up in my GWT profile. Now over time quite a few of them have dropped away, but according to Remoovem I've still got a 73% link percentage score for this particular anchor text (which is my main keyword), along with a 55% root percentage. Obviously this is a Bad Thing. What would be the best way to combat this over optimised profile?
Disavow the links? Leave them be and work on more exact match links? When I look at some links listed in GWT, I can't find the link to my page anywhere in the source code. Can I ignore those domains or should they also go into a removal program? I've not received any manual penalty or notice in GWT, though I did see a drop of traffic last year around the early may 'Phantom' update. From which the site has never really recovered.

My business is based in Suffolk, UK, but I serve an area that includes Essex, Cambs, Herts and Norfolk. I've been making an effort to include a constant NAP across all my local citations for Suffolk in an effort to rank better in local search.
However, what effect does this have on pages when trying to rank for searches for areas where I have no physical location? If my entire site has NAP across it referencing Suffolk, does this impact the ability to rank organically for areas outside Suffolk? If so, what would be the best practice for increasing organic rank in these areas?