The Shaping Focus feat from Ultimate Magic (+4 to druid level for purposes of Wild Shape up to character level) does not take into account if other classes add to the Wild Shape ability. For instance, I have a prestige class (Arcane Heirophant) that I added that adds to the druid level for Wild Shape. If I'm Drd3, Wiz3, AH3 and I take that feat, it should give me Wild Shape as a level 9 Druid. Instead, it gives me Wild Shape as a level 10 Druid (adding 4 levels instead of 3, and going over the total character level).
Alright, I have modified the feat to take into account the possibility of other things adding extra levels. Have your class add Extra levels to the wild shape abilities before Pre-Levels 5000 and the feat should take them into account. Hope that helps.
I also made an adjustment that allows you to pick a class ability and add/subtract extra levels to it, in case that's convenient.