About incoming links from same server/IPs, if these are actual sites with real content and a real white hat purpose and not spam networks, then there's nothing to worry. If G hasn't picked it up after a long time then it can be the way the links are structured that isn't seen by Google. Also G may not always show all links and it may take even more than a year to show a link, even if it's a good link in a page that is indexed. The link report in WMT can be really buggy.
Ranking well in Google comes down to links and on page structure. It's that simple, and it's beautifully simple too.
Do you have the type of links that give you butterflies in the stomach when you notice that you got them and even every time you visit the page where your link is?
Do you have content that has so many FB likes that you feel like buying Facebook stock shares?
Is your site navigated in a way that allows for PageRank to flow to where you want it to flow?
Do you have unneeded internal (and external) links?
Is your site slower than 2 seconds to load (although this is a minor ranking factor but hey 'we optimization now')?
Are you keyword stuffing your headings? By the way, use of headings is overrated these days, and only good for semantics and long tails and only if you play your cards right too and don't keyword stuff the hell out of them like most people do.
Way too much stuff going on. I haven't seen your site but my guess is that you're not under a filter (not a penalty, as a penalty is manual). You just lack off page and on page SEO.
[edited by: aakk9999 at 9:23 pm (utc) on Apr 9, 2015]