According to the picture the back side of the large motor mount that faces the lay-shaft gear looks like it hits the mount, is that a mark on the mount from the gear hitting it? There should be a shim washer or washers that will not allow the shaft gear to come close to the bearing or mount on the back side.
CLICK PHOTO TO ENLARGE:

You also should not be able to move the lay-shaft back and forth much and once you get the alloy spur carrier FG#6439 it wont move at all.
1st thing I would check is that the motor mounts have not moved shifting the whole motor to the left. This will cause the gear to hit the shaft also like you see.
Unloosen the motor mounts and let the spur-shaft gear rest against the diff gear. Now, you can slightly manipulate the gear mesh to get yourself enough room away from the upper A arm shaft. Make sure the gears are set or meshed so that they are as perfect together as possible with a small amount of room between the gears so there is no bind but not to much slop. Use a slim business card and squish it between the diff and spur-shaft gear. Now with your third and fourth hands tighten one of the screws so it doesn't move.
Use the FG shims #6745 to get the gears to mesh the best possible.
The bend in the plate is not that much and its aluminum - unbend it.
It may of had to be bent for it to fit the hight difference of the alloy mounts.
If its not bent for the mount to fit then heat it, stick it between two pieces of flat wood, and hammer it together. If that doesn't work try two pieces of flat steel.
You have the alloy rear uprights! The next best upgrade to eliminate gear rub - And the only way to eliminate it - is to get yourself a set of alloy risers, FG #7478 seen here -
https://www.largescaleforums.com/forum/showpost.php?p=16507&postcount=6
Like these:
http://www.rcnutshobbies.com/FG_PARTS_07000_07500-Rear_alloy_upright_lengthening_set_2pcs.html
Made for on road camber they allow off road to raise the shaft and get it out of the way, but you need alloy uprights for them to work, and you have them.
Use a sealant on top of the plate screws to keep them from vibrating out.
Get that horrible KN filter off and go back to the original and get yourself a redneck
http://www.davesmotors.com/store/product707.html prefilter to go over! That KN filter will suck deadly crap into your motor. M2C.
