Rhys one more thing. Did you torque down the flywheel bolts with a torque wrench? We torque them to 65ftlbs. Also, what was the condition of the flywheel?

You will be going through the bedding in process now, but if it doesnt improve after a few weeks. I will suspect the flywheel.

Changing the engine mounts and diff mounts as mentioned by Strubaru is spot on as well and is a worthy upgrade. This guy knows his stuff.