My suggestion: Get a piece of wood about the height of your transom, and a C-clamp. Mount the xducer to the wood, clamp the wood to the transom, then start playing around with positions.
Most manufacturers say to mount the xducer off to one side to avoid the turbulence generated by the motor. Seems to me that most of that would be behind the motor, but, then again, I haven't really tested that.
As far as the transom lifting at speed, well, that's what you want. The transducer should be mounted approx even with the bottom of the boat, so at speed, the water should be rising coming off the aft the hull, keeping the xducer face in the water. Play around with height until you get the best performance for your setup.