How's warmup running? Ie open loop running? Run better for the first few minutes until the blue coolant temp light goes out?
Any codes?
Taking the plugs out is a great indicator of overall running condition, also gives you a good opportunity to see how much oil is in the intake manifold. There is no EGR on the MR motors (not the NA ones at least). Injectors can always cause rough or unequal running, causing vibrations. A universal scan tool can do a quick cylinder balance test, which can be a good indicator of compression, injector flow rate (or lack of), valve seating etc.
Motor mounts transmit very noticeable vibrations when they go bad. You can grab the motor and shake it front to back motion and see how easy it is to do that. Watch the mounts while this happens, there should be some movement, but if you see cracks in the mounts or excessive movement then you have a problem. You would need to take out the intake and battery to get a look at the tranny mount. They are soft as butter stock.