There is a bit of sealer between the two case halves from the factory, and putting it back together says to put some more inbetween. With my motor, the oil pump was the issue. A couple of extra bolts we overlooked. Also, I second the "missing bolt" theory. We also had to remove the alternator, even though the FSM said we didn't have to.
Hammer is recommended over a large prybar, since there's no real good place to pry on the covers.
If all else fails, use a little heat on the seam. Just don't overdo it. To correct another posting, metal expands when it gets hot, and shrinks when it gets cold. Different metals expand/contract at different rates, depending on their composition.
Luke M
Used to have a 1979 CB750L, sold it as a parts bike, now riding a slightly modified 1984 VT700C. Network/Field Engineer. Central OH, USA, Earth, Sol System, Milky Way Galaxy, Universe.