I'm not good at English but, got the feeling that Jonathan and Martha are not dead.
You got the right idea -- the guy was talking to "our" Clark, and of course his parents are still living. The confusing part might have been that our Clark was telepathically keeping in touch with alt-Clark, and even managed to transfer the pain of Kryptonite to himself so that alt-Clark could function. Which is one heck of a trick, but hey, when you've got telepathy and body-switching already, what's a little bit more?
Yvonne, I've said it before and may say it again: This was *intense.* Good job.
So... when do I see more of this????
PJ