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No it has no relevance at all. Majority of the time people that want to link their sites together, they are under the same host. With the whole same host or IP and linking one another not coming up as a problem, it should be noted that it won't hurt you in any way. But things could easily change or there might be variables we don't know. If you want to play it safe, just make the links one way and not reciprocal.

Sorry Johannes I think I confused matters... I didn't mean there is spammy content now, I mean the spammy content that you removed. I'll be cursed for saying it but it's quite possible some of that spammy stuff was working if there were exact matches in there then which aren't now. Google isn't perfect yet so unfortunately some spam does still work (for now) though it will likely hold risks too. My suggestion with that was to look at the spam that was removed and figure out how to incorporate some of it back into the site in a non-spammy way. With regards to the link numbers, yes if it was me I think I'd remove at least some of those footer links too. My mistake with the rel canonical, I didn't spot it but just noticed it was a bit lower down. The duplication could well be the issue, but if that's the case and the dupe is no longer there then it should sort itself out pretty quickly.