I need a micro controller with a USB slave and Host interface (i realise that is not on the Arduino) to act as a go between a PC USB port and a USB mass storage hard drive in both directions.
Although you can build such a device with a Leonardo (has USB slave capabilities) with a USB Host Shield (providing the host part), you probably won't get happy with it because the Arduino will be the bottleneck. It's running with 16MHz, todays USB storage devices operate at 480Mbit/s transfer rates, completely out of reach for an Arduino to only transfer it, don't talk about doing something intelligent with it.
A proof of principle even running slow will be enough to show the system works and then it can be built into silicon which is where it would finally be at home.
I also said this is not limited to the Arduino but at the moment I am more interested in really understanding the mechanics and protocols behind mass storage over usb and to be able to interface at this level.
per command level.
Don't expect help on this forum if every participant have to sign non-disclosures. If you're already going for a patent, why do you need such basic help?
I was not saying everyone has to be willing to sign a non-disclosure, and I am more than grateful for any advice especially the free type but I also wish to protect my investment and creativity of concept so do not wish to give the full project total disclosure to Joe Public!
I am however willing to enter a business relationship with the right expertise to get this "Simple and Basic" project as you think it is to hopefully one of them simple (why did I not think of that) commercial products that end up on the World market (but only time will tell if this ever happens and the right investment 
I understand programming and micro controllers all to well but my expertise is not with the mass storage class and USB protocols and need a platform that may be to start from even if its not the finial product, but now that I had some useful directions to explore I will endeavour to learn it myself if required, however with an Expert in this field time to market would be "accelerated" and that can make the difference from a good idea to a million bucks I guess (here is hoping)