I have a '79 650 I have done this to
Are u talking a 79 650? The 80 up 650's the box is separate. Only have had one 79 parts bike so not familiar with them but know they are quite a bit diff.
Terry
Huh.... I didn't know they were THAT different. That goes to show why no one should listen to me. 
From the looks of it, the '80 and up CB650 inner fender should work if your completely removing the airbox.
I own a '79 and a 81, and the differences are massive and many.
Amony many is :the tank, seat, headlight ears, trippletrees, forks, swingarm, rear rim diameter('79 is 17" 80+ is 16"), airbox fender(front and rear), footpegs, frame...
and the list continues.
OOh. did I mention the '79 is the only year to use those sidecovers(US, never seen Z model sidecovers in person... yet)
I used the inner rear fender section off a '80 cb650.
Battery box has a minor amount of interference, but nothing major.
I plan on doing a custom battery box/elecric box soon.
l8r