Again, thank you for your feedback!
I may have changed a few of the product codes which should create a 404, but i had a catch all redirect so now they are soft 404. I only have 29 total, or 20 more than when i started. I will make sure to fix, even if this is not the cause.
With 1200 pages, and 600 products I am confident that +20 soft 404's is causing 25% week over week traffic, hurting me from 2K a week to 1K a week.
See screenshot from webmaster tools
I am so puzzled by this.
I think that I have just shocked the engines. I have done it before, hurt for 6 weeks, then back to normal, hopefully better (fingers crossed).