I'm in a similar boat. I did a valve adjustment last November as well, and since then I've had what sounds like knocking. It's more pronounced on the left side of the bike. At the time, I was pretty darn sure I did everything right but... still a worry. I've got perhaps a thousand miles on since then. I've done a starter valve sync, a balance shaft adjustment, etc. and while it's better I still have what sounds like knocking.
I used my mechanic's stethoscope and I do hear knocking on the left but I can't really pinpoint where it might be coming from.
I don't think I have an oil leak so I don't think it'd be the intermediate shaft.
Any thoughts?