Yes Mark yet another factor and that's a thing when working on bikes from our era on top of the other stuff.
Nowt worse than folk who think battering motor cycle parts with a hammer is the solution.

I think of spinning true & balance as two different things. & i wouldn't know how to alter the balance factor--drill holes or add weight? i guess. I remember when we were bucket racing "road racing 100cc" my boys mate had his Suzuki TS100 6 speed in an RG50 frame which was light & good handling but vibrated bad with everything mounted tight & just seemed to be the motor/crank wasn't balanced to suit that spindly light gauge steel frame. Well--that was what we thought at the time. Mind you it was revving to theoretical 12-13000 instead of half that as a trail bike. My one was/still is ion a Honda CB125 frame & is holding the frame together like the Honda motor used to & is smooth 'as' with little vibes. Same motor i used a crank from one side of a Yamy RD200 & was silky smooth but less stroke if that counts. Funny what works & what doesn't. Fit a ballancer like an MX360, that'll stop the vibes.

I agree that balance factor and true are two different things. 

I have an very old book somewhere that describes balance factor and how to modify it...  the thing in my mind is Yamaha engineers knew what they were doing...  which may have not been the case for engines built in the early to mid 1900's or when modifying a very old engine for racing.  Which is what the book I have covers. 

I can't imagine changing balance factor on one of these Yamahas is a worthwhile pursuit in most cases?  If someone wants to try it though, it's their time and effort.  It is interesting that the original question was posted like it was a common modification when my guess is most members here have never heard of modifying the balance factor and probably nobody (other than perhaps OP) has ever done it?  Maybe we'll all learn something?

I can say from experience that checking and precision truing of the crank is definitely worthwhile.