Found a solution to tracker not going up for mods. The tracker for the achievement reads your progress based on how many mods you have unequipped. If you have several mods equipped in your weapons make sure to remove them before you make your next mod. Once you make a new mod your achievement tracker should match how many mods are sitting in your inventory. Friend just tested and he jumped from 53 percent to 73 percent on the 15 mod achievement.
Be sure to only make mods in your own world. Same goes for purchasing armor.
Boss weapons with mods do not count towards this achievement at the moment since you can't remove them.
This solution will not help anyone who has already collected all mods in the game.