Sorry, looked back and realized your timing belt was not even installed in that pic...my mistake.
I tore my original mounts near instantly the first time I pulled a 2.7t. I know now they are not designed to have ANY upward force on them whatsoever. I learned the hard way.
I had no issues with my shifter (knock on wood), at least with clearances other than the o2 sensor which I bent out of the way. If there is anything you'd like to reference as far as pictures go, let me know and I'll go out and snap whatever you need. I did not, however, change the stock shifter mechanism whatsoever from the point I removed it from the donor car. I simply unbolted and swapped it straight over. I didn't even update the bushings or change to a short shifter (which I sure hope I don't regret down the line). Have you tried shifting it with the engine running? All four wheels of mine are off the ground and I was able to start the car and put it into each gear (as far as I can tell) with ease.
EDIT: sorry, your previous pic just appeared. I see now where you are rubbing. It seems something must be installed incorrectly. Mine bolted right up with no issues there. Yours should as well. In a bit, I'll go out and take a look to see how close mine is. ***ALSO*** I too, first installed that cross rod in the incorrect hole. Don't know why the other hole is even there (to screw stuff up) but it throws everything out of whack. I bet that's what is going on here.