Just because a link is added to content after the content already exists doesn't immediately qualify it as spam. 99% of links being spam is a pretty massive assertion, is that anecdotal or backed by any actual data?
It does however make it very difficult to gauge who is a legitimate linker and who is not.
All I'm really saying is if you're starting now with all of the years of random linkspam backscatter is that you are in for a rough ride.
As an aside, you have use Ahrefs.com to get pretty decent tracking of when links appeared since it started (I think ~18 months ago or so). Given that the rate of spammy pages is increasing extremely fast and old spam pages are dying off, I imagine that in the not too distant future you'll be able to get decent link history for many sites.