A few more thoughts.
Some other members on here have fitted a replacement engine mount spring and found it was stiffer?, resulting in vibration being experienced that wasn't present before.
I checked out the workshop manual (available in the Download section of F.F.).
This lists 3 possible causes of engine vibration.
1. Loose generator bolts.
2. Blower (i.e. fan) blade assembly out of balance.
3. Incorrect clearance of rear engine mounting rubber..........
Good move to check for possible metal to metal contact in the rear mounting.
The problem I mentioned earlier re. vibration on a Fiat 600 was caused by someone inserting a washer into the mounting to reduce engine rocking. This washer meant that there was no clearance on the rubber buffer contained inside the mounting which is only supposed to come into action when the mounting is compressed i.e. like a spring assister.
(I'm aware the mounting on the 600 is different to that on the 500, but the principle behind it's operation is, I believe, similar).
Another point is that sometimes replacement engine and transmission mountings are not always made from the same stiffness (Shore No.) of rubber as used in the original parts.
When fitting any new mounting, engine or trans., its considered good practice to loosen all mountings, rock the engine trans. unit about, allowing it to find it's natural positiion, then tighten all mountings. Same as when fitting an exhaust system. Incidentally, the 500 trans. mounting frame/crossmember has slots where the trans mountings attach to allow a little adjustment to prevent pre-loading the mountings.
If you still have vibration problems, I'd suggest disconnecting any item which might be transmitting vibration into the cabin, one item at a turn until the vibration disappears. You could start with the gearchange rod (although it has rubber in the coupling adjacent to the trans.), then the clutch cable (is there any difference in vibration when the clutch pedal is pressed?), followed by the speedometer cable and any other items that might be the culprit.
Another item to check is the rubber? covered plate at the rear end of the tunnel where the gearchange rod., clutch cable, handbrake cables etc. exit the car interior and connect to the engine/transmission - could anything be wrong here, causing the vibration issue?
Is it possible that your lowering plate is the root cause of the problem? Maybe this is putting something under strain resulting in the transmission of vibration into the passenger cabin? It might e.g. be twisting the trans. mountings? Or trying to bend the gearchange rod? Or forcing the gearchange rod against the cover plate mentioned above?
If it was my car, I think I'd try removing the rear engine mounting, supporting the engine on a jack at its normal installed height not where it's at with the 18mm lowering block in place. If the vibration disappears, then try lowering the engine by 18mm and see if the vibration recurs - which would indicate that lowering the engine caused the problem.
Remember that all parallel twin cylinder engines vibrate, usually very badly - just try an old Triumph or Norton motorcycle vertical twin.....
There's a number of different types of imbalance, you can't eliminate all of them (although the inclusion of balancer shafts in the design can work wonders), some of these forces vary with speed, some in direction and whether the engine is delivering power or is on the over-run. The best anyone can do (manufacturer or engine balancing specialist) is try to get the worst out of balance forces to occur where they won't be too intrusive or damaging. e.g. smooth at idle speed, no severe vibration at engine speeds used normally.
Some Fiat models incl. 4 cyl. ones had a habit of breaking throttle return springs due to vibration, Fiat's solution was to fit a rubber insert to dampen out the harmful vibrations. As I suggested earlier, it might be worth trying to rubber mount the rear view mirror is if it's shaking is your main cause of concern?
AL.