that doesn't sound like significant enough changes to cause a 4 position drop, could just be fluctuations.
careful with the directory site link building! don't link to the homepage if possible.
why is the traffic higher, are the visitors going to any specific landing pages that are well optimized?
I would look into noindex,following the tag and category pages, install the yoast SEO plugin for wordpress and it will automatically do a lot of that for you.
https://www.google.com/#q=site:supereyes.com&hl=en&tbo=d&ei=Q0T4UOzGFsOOrgeciIGwDA&start=70&sa=N&bav=on.2,or.r_gc.r_pw.r_cp.r_qf.&bvm=bv.41018144,d.bmk&fp=86d36ab695df5dc2&biw=1920&bih=937
a little bit of stuffing in the footer, i would remove that:
Milwaukee LASIK | Milwaukee Eyeglasses | Milwaukee Contact Lenses | Milwaukee Optician | Milwaukee Optometrist | Milwaukee Vision Center | Milwaukee Eye Doctor | Milwaukee Ophthalmology | Milwaukee Intraocular Lens | Milwaukee Cataract | Milwaukee Glaucoma | LASIK in Milwaukee | Eyeglasses in Milwaukee | Contact Lenses in Milwaukee | Opticians in Milwaukee | Optometrists in Milwaukee | Vision Center in Milwaukee | Eye Doctor in Milwaukee | Ophthalmology in Milwaukee | Intraocular Lens in Milwaukee | Cataracts in Milwaukee | Glaucoma in Milwaukee