Reluctant to offer any thoughts, as you have done so much work already, but here goes. Hope they are useful:
I have been studying Lancia V4s, crankshafts and balancing, analyzing how Lancia addressed balance in the engines.
So... did these engines vibrate? Yes, they all did - but it was more from being a variation of an in-line 4 than the V. So it shouldn't vibrate more than a 1200cc conventional inline engine - which should be more in the nature of a buzz than a vibration. All the V4s will vibrate, but Lancia went to very interesting lengths to moderate that. The engine mounts are designed to reduce vibrations in two different ways, a composite solution. So the following questions:
Do you feel it in the gearshift lever more than atop the engine?
Consider disconnecting the driveshaft, run the engine and gearbox and see if the vibrations are significant at certain rpm.
Is the crankshaft original, or was it "rebalanced" at some point?
Were the connecting rods changed? Lancia had specific weights for these, but more importantly, lengths. Sometimes people fit new pistons and move the wrist-pin (gudgeon) lower, and shorten the connecting rods. This impacts vibration, surprisingly.
Piston weight changed?
Years ago had a serious vibration issue in an Aurelia, which was almost impossible to get rid of. We finally found that an accident on the front right had shifted the left motor mount a bit, throwing off the axial alignment of the engine:rear transaxle. We only found this out by placing a laser on the crankshaft centerline, and noting when the block was installed, the alignment was 5" off to the side at the rear. Might you be able to check axial alignment coming off the gearbox to the differential? Imagine some large disc, bolted onto the back of the gearbox (minus the driveshaft) with a 90º hole in center, with a small laser.
Check the ancillaries - flywheels and fan especially. Sometimes...
Hope this helps.
Geoff