Thanks, Matt. BTW, I like your website - I was browsing it yesterday and plan to print out the Electra maintenance page. Nice bikes!
First: I'm using the decompressor to stop the engine now, which has resolved the "reverse" issue when using the kill switch. It may be my imagination, but the engine seems to start cleaner now, too.
Second: Closing the choke just made a difference because the engine wasn't as loud when it was closed. I don't know if there's a leak around the intake system. I ordered Pete Snidal's manual, which just arrived, but I haven't had a chance to read it yet (and didn't know to check for leaks).
Third: Per your suggestion, I removed the primary cover again last night. While it was off, I readjusted the chain (loosening it) after checking it in multiple spots this time. The only thing I noticed was that the oil was already darker (I just changed it).
After replacing the cover, I started the bike again and the noise continued. Aside: This may not be an issue (or at least a related one), but the rear chain engaged even though the bike was in neutral, moving the tire slowly.
There's always a possibility that the sound isn't coming from the primary area, even though that's what it seems like every time I've checked. Another user suggested that I buy an automotive stethoscope to help find noises, which I plan on getting this week. I also posted this message on the "RoyalEnfield" Yahoo group and users suggested that the issue could be related to the starter sprag or valves.
That'd be great if your friend has a chance to listen to it. Maybe he'll be able to discern what it actually is.
While the primary cover was off, I took pictures - They may show something that I'm not seeing. As soon as I get them off my camera, I'll post them. Thanks again for your help.