Yep, it's a hard design to get to seal. But, I did this on my '74 KZ400 about 5 years ago, and it's still leak-free! But, I was younger and dumber then, and am not sure I'd do it again this way: I used Permatex High-Temp RTV Silicone Gasket Maker (red). I filled the groove with it and just did a very very thin 'skim' coat on the groove edges (the surface which touches the head) and around the rubber-coated metal plugs.
I didn't allow any cure time, but reassembled the cover right away. I'd let it sit for 24 hours before firing it up, but when I did this before, it was part of a lot of other work, so it sat alright, but not by a consious decision. I got virtually no 'squish out' and like I say, it's still leak-free today, but if I had to do it again, I'd probably just go ahead and buy the O-ring.
More recently, I redid the leaking top end on a SOHC Nighthawk 650 and it's the same thing - a complex O-ring all around the rocker box. In this case, I DID buy the new O-ring. No further leaks, and no chance of silicone getting where it shouldn't.
Just my two cents.
Kirk