If your backing plate goes on the studs for the transom assembly there is not reason why the engine shouldn't able to be lined up. You probably just need to move the bearing around a bit to get it lined up. Also, the transom should be a minimum of 2" thick and a max of 2 1/4" thick. If its more than 2 1/4" you will not have the proper amount of spline engagement of the input shaft of the drive. I am assuming that since you said the stringers were replaced then the front mounts have not been drilled yet. So lining up with the from mounts wont be an issue. A few pics might help us as well

pulled transom assembly redrilled holes and now everything lines up beautifully

thanks to all for the input