Thanks everyone for your Help, I did get everything to work.
First I got wireless to work using Companion, but I wasn't going to give up on getting usb to work as well.
I finally noticed on the Nexus 7 that on the Notification Dropdown it was signing onto my PC as a Camera, clicking on that sent me to a screen that gave my a choice to of Camera or Media Device checkboxes and gave me a different set of folders for Nexus 7 in my PC file directory program. Yay! its working.......
Not quite, I opened Calibre and I got a popup asking if I want to manage Nexus 7.
I picked no because my Library wasn't configured the way I wanted. I could send files to the Nexus 7 but now it wasn't detecting it as a device. Turns out saying no configured Calibre to recognize Nexus 7 as an Ignored Device, unchecking that fixed the last problem.
I hope all this information will help others and Thanks again.
That's my story and I'm sticking to it. ;P