My TR3A was bone stock, and it vibrated so my key chain would rattle and shifter buzz. The factory did install a little spring and plunger to reduce the shifter vibration. My TR2 was balanced during the engine build. Being my anal self, I took every part, including the rod nuts and bolts, down to less than 1/10 gram. I have no sound or noticeable vibration at all...even though the TR2 does not have a spring and plunger.
The balancer on a TR4 is a bit of a joke. The tranny has to physically move some for it to work. If it moves at all, you have vibration, so all the balancer could do is reduce the level of vibration.
On utube I found an interesting video showing the standard factory while they were building our TR's. It even showed the balancing operations and told the standards they balanced to. They were trying to impress the watchers with the level of detail, but I was not thrilled...the parts tolerance was often more than an ounce per part. They DID match the rods and pistons into sets to try and reduce the overall imbalance, which was better.
The shaking is due to imbalance of the engine and/or flywheel. If you have ever had the wheel faced when replacing the clutch, then it needs to be re-balanced. Few...almost none...ever bother with that, but that is where most tranny vibration originates.