Adding that mounting bracket is a good idea as it will move the transducer back away from the transom and more into the cleaner (air bubble free) water flowing under the hull. The downside of this is that you may have to trim the motor out a little farther to keep from blocking the Si sonar to that side.
As for the roostertail: did you install the black rubberized piece in the transducer? This should have been in its own bag with the unit. It fills the gap made between the transducer and the transducer mounting hardware.
As for the mounting height of the transducer: using this bracket should allow you to be able to mount it a little higher than what the instructions state, but I would still start their to begin with.
When you are done and have it all tuned in, please post some pictures of the bracket and transducer as well as some overall pictures of the transom. I think that many aluminum boat owners would be interested in this. Of course, pictures of the fish you catch are always welcomed!