here's my halfpenny worth,
The so called 'blisterback' crankcases came in during 1961 at about No.94500, very, very few 99s have them. The 650 crank won't fit in the earlier ones (Well actually the crank will, but if you put the rods on, it won't turn!).
The crankshaft is OK IMHO, the stuff about the rod failures being mostly due to lubrication problems is BS IMHO, I would call that a big end failure, I've had two go, both on the timing side about 1.5" below the small end, I've got one somewhere, will post a pic if I can find it, the shells were perfect, so much so that I used them again in another rod with the same crank in a spare case. I agree not to use Carillo rods but not for the same reason, I tried it and the vibration was HORRENDOUS even with the crank & rods dynamically balanced due to the greater reciprocating mass.
If you do put a 99 top end on a 650 be prepared to modify the barrel spigots as the rod cut outs need enlarging.
The 650 head goes straight on the 99 barrel, 1/2 true, the early ones will that have the spigot recesses will, not the later post 1966 ones.
With a 650 crank, change the oil pump for the later one with the wider internal gears, don't just speed up the small one, you'll just end up with a frothy oil tank (at best....).
I now run a hybrid 650/99 motor in my 99 (650SS bottom end with with new 850 type rods, married to a 1960 type big fin/valve pre-downdraught head and a single 30mm Mk1 Concentric. Pulls like a train with a 21 tooth sprocket, faster and smoother than the old 99.
Good Luck!

Oil is always cheaper than metal