Matt,
I am no engineer, but I can tell you what I know and what I see.
What I know:
I know that any cushion you put between the motor and frame, and the trans and frame will allow the motor and trans to move around.
What I see:
First, your rod linkage is mounted to the trans which is good and bad. The good is that when the trans moves, the mount moves with it. The bad, is the rod linkage does too. Your rod should come parallel to the setup(or as close as it can to that). The way you have it, when you move the trans(torque) your rod will move in two directions at once, sideways and front to back(because of their mounting points). If it is parallel, it will only move sideways. and you will have very little movement of the shift lever in the car. The rod actually moves in an arc, but the moment of moving is very slight(I think I said that right). What it boils down to is very little movement of the gear shift lever.You will probably feel the gear shift lever move around whenever the trans moves as it is.
Second, because your rod comes in at an angle, the heim joint has to move in two directions to get the shift linkage to move in one when it goes side to side. That means your neutral gate is at an angle in the car, not truly side to side. I am making an assumption here that the neutral gate is the lateral movement of the shift linkage on the trans. I would think that the way it is now, would put a bind on something, moving like that. The movement of the rod should be the same movement of the shift linkage. All of these mis alignments, seem to me, to put a lot of pressure on parts that shouldn't be there(the pressure).
What I know:
I learned with my cable linkage that alignment is everything. Even cables can get messed up if not aligned properly. Cables that are stretched out straight act pretty much like a rod if supported right.
What I know:
If you eliminate your movement of the engine and trans, you will eliminate the movement of the rod(above). I mounted my trans and motor solid to the frame. I feel virtually no vibration at all when driving on the street. Under full power is another story. At red lights at idle, the car actually rocks a little due to the rough idle and torque being applied by the motor. I call it a dance and it gets considerable notice at red lights by other drivers. Remember, torque and vibration are two different things. Now my motor is internally balanced, but other engines apply counter weights that smooth out the motor pretty well. They put rubber cushions to eliminate all the little vibrations and smooth out the torque when applied. Remember, we aren't driving luxury cars.The suggestions made earlier to control the rock of the engine do the same thing as my hard mount.
Anyway, that is my take on it. Hope this makes sense.
Bill