I believe in the Ashenden interview, or in the extended link, he points out how many of the tests showed likely EPO use, but could not be considered + under UCI rules. So it was likely many more than 13, but the heaviest dopers showing up as those 13.
As to cleanest years, I agree with BroDeal, probably in the 1980's, as cortisone, steroids and amphetamines were all there were for years. They were used a lot however at times, but not game changing the way blood boosters are. Lemond was clean, Hinault very likely clean in 1985 and 86, maybe, possibly in 82. Joop and beyond? Who knows?
Dirtiest probably was 2003, that list is bigger than 1996 or 1998. The years really from about 1992 to probably 2006, or even the present have been pretty obviously dominated by a lot of blood doping. Just a few more cheats caught in the last couple years, and much more microdosing.
Cadel, Sastre, VandeVelde and a few others deserve to be called "cleaner", sure. I don't have much faith in Wiggins, but maybe, who knows. Two top 50 riders I would go out on a limb and say are riding clean these days are Cunego and Deignan. Several more are likely clean, but not getting results or high placings anywhere.