VIBRATION - deciding too much; and living with it.

[pekingduck]

The 4-cylinder vibration also annoys me, though most people don't notice it.
If you are saying the vibes have gotten worse, was there a point it changed noticeably? And did you change anything else?
Stock mirrors are an engineered part of the handlebar dampening. An aftermarket exhaust or engine guards can change the harmonics. Did you check torque on engine mounting bolts? That's a critical point on the VFRs and ST1300s.
If the vibes are normal, there's no fear of damaging the engine.