Ok everyone the problem is fixed. I decided tonight that really didn't want to return this case so I was going to try my best and fix it. So this is how I fixed it.
First off I took the motherboard out of the case. Then I made sure all the standoffs were tight using the key provided (not hercules tight, just enough to feel a bit of pressure). I used the standoffs that were pre-installed on B & F not sure if its needed but I did it.
Then I installed my graphics card on the board whilst out (always so much easier).
Since I noticed the angle that my motherboard was sitting I decided to try and manipulate the m/board tray a little. So I got my fingers in the cable management openings and pulled the metal up. I did use a bit of force but not too much. Since the board seemed to be sagging at the back I was trying to raise it some. I think this helped.
I then put the board back in. There is a tiny bit of play on whilst on the standoffs so I used it. Once I was happy that the card was lined up I began screwing down. I screwed B and F first, I was firm with these it felt right. The remaining screws I was gentle. Not too much on any screw.
Now the back screws did give some me bother.As I was tighten them I noticed the were pulling the GPU mounting bracket a little further back. So what I did was get my fingers underneath the tray through the openings and push the standoffs closer to the screws. The back screws I didn't tighten much just enough.
After I was finished everything felt solid and I was happy enough.
Please do not let this put off this case, it really is an amazing case. A pleasure to work in. I just happy I didn't have to return it.
Hope this helps any other poor soul.