I already understood that you were going to attach the torque tube to the cradle, but when you attach your torque tube to to the cradle the linkage will bind up because you have two extra links that make the linkage rigid.
Correct me if I am wrong, but I beleive you are planning to put the pivot point of your cradle near the bottom of what was the motor board inside the hull.
If the torque tube is attached to the cradle with a rigid mount, then the shaft must pivot about the inner pivot point, near the bottom of what was the motor board. If the two links that go forward to the transom aren't in line with that inner pivot point the linkage becomes rigid. It can't move without putting high forces in the links. In a car suspension there are ball joints that allow angular movement of the upright, but your upright is rigid, it is welded to the torque tube, so no angular motion is present in that section.
Right now your linkage will move, only because the torque tube isn't firmly attached to the engine cradle. If you attach the engine to the cradle and leave the torque tube free, you will need a coupling that will allow the shaft to move relative to the engine. You will need both axial, radial and angular misalignment capability in the coupling to make it work. If the engine is rigidly mounted to the shaft, then you will need to have some type of mount that will allow it to move relative to the cradle. Neither is a good solution.
You should probably go through the range of motion with a scale drawing to see what is moving where, but right now the kinematics are such that it will bind up unless there is a lot of slop in the joints. You have Heim joints in the links now and that doesn't allow for any slop.
In order to make it work the transom mount links need to have their pivot axis on the same line as the cradle pivot. If they don't you have a static system and it won't move unless something bends or breaks.
I would simply get rid of the transom links and design a structure that holds the torque tube without them. Keep your pivot to one axis and it will work. Otherwise you are just going to have problems.