Doug,
Bruce mentioned the brackets which are mounted onto the transmission tunnel. The holes you are trying to alighn with are in those brackets. It can be quite difficult to align them properly but, I developed a good technique. I found the holes in the clamps and put a nail into each. You can use the nails to position the center tray and drill any holes which may be required. Once the tray in in position with a nails through the holes, remove one nail and replace it with a screw. Repeat the process with the second screw. I hope this technique works for you.
Ted
1969 280SL w/ spare tray
