I have used Stable Matting in the rear of mine. Keeps the noise down a treat. Only problem is you need 2 6x4 sheets and end up with quite a bit left. Most Horse places will sell you a couple of sheets. This is like the stuff I used
My TD5 did a simalar thing started to mis-fire about 50mph in 4th gear. But some injector cleaner and a change of fuel did the trick. Used to use Asda but runs so much better on Shell.