I assume that you are referring to the ply board that is laminated in to the transom? Or are you referring to a separate piece of ply that is added against and/or on top of the transom? The latter has been added by a former owner and is not a standard piece of a Wayfarer. Get rid of it. You need to spread the load by adding (or using existing) ply *inside* the tank.
The piece of ply that is laminated into the transom is symmetrical along the middle of the boat, on both sides of the rudder pintels. You can’t see it from the outside but if you stick your head in the tank you should see the thick areas in the GRP where the plywood is. Though the laminated piece of ply is not intended for motor support but to strengthen the transom for the rudder we can use it as such. The width of the ply piece varies because the builder did not have an engine in mind when he put it in.
Just put the engine bracket as far out as possible, but make sure all four bolt holes go through the laminated ply piece (the one laminated into the transom). If for some odd reason that gives a bracket position too close to the rudder, you may need to add some additional ply to the inside of the buoyancy tank, next to the laminated piece that is already there. In this case two of the bolt holes go through the laminated ply and two through the additional piece. Under no circumstance try to remove or replace the laminated plywood. That is a major repair and would, at the very best make your boat subject to re-measurement. In the unlikely case that your boat has a very small piece of plywood laminated into the transom, you could use a full size plywood counter plate for all bolt holes.
The height of the shoe isn’t critical because you can adjust the height if the engine mount plate. If the top of engine mount plate is about level with the transom it is OK. In my case the holes in the engine mount were not drilled and positioning it at the right height was easy.
I have also seen boats with the engine mount fastened off center to bring the engine further out. This too may help positioning the engine when a boat has a small piece of ply laminated into the transom. (off center relative to the bracket obviously).
The engine position isn’t that critical at all. You just want it far enough to the side where it won’t ‘bite’ the rudder, and deep enough to keep it submerged in a chop. But don’t put it too low, that may make it impossible to tilt it forward (to lift the engine out of the water while sailing). Either the transom is in the way of the engine head, or the screw drags through the water all the time. In my experience having the top of the engine mount level or slightly higher then the transom is a good position. It is not a matter of hundredths of an inch, just have it about right, give or take an inch.
And don’t forget: measure twice, drill once.