vibrating 106Gti

My son's 1997 R reg 106 GTi, 91,000 miles on clock has started to vibrate when engine turning at between 1500 and 2000 RPM. Feels and sounds like the whole car is vibrating when you are inside it but doesn't sound unusual from outside the vehicle. It makes no difference with the clutch engaged or depressed and it has not affected the performance. It all started after replacing the 'seal' (like a compressed Brillo pad) between the back end of the manifold and the start of the exhaust pipe along with the springs, nuts and bolts with a shoulder preventing it being tightened to far. The exhaust is not touching the bodywork anywhere and has been checked with the engine running and being revved. Help!