There's also the possibility the controller chip is bad (it happens occasionally) or there could even be something the matter with the socket (unlikely but not impossible). Because of the possibility of the controller needing replacement I guess I'd tend to prefer Ian's offer. It means waiting for delivery from Switzerland but it saves you having to flash a fresh blank controller. Your call! Also I'd say the capacitors are the least likely suspects unless they appear physically damaged. Pretty rare to find a bad ceramic cap.
I can not say enough about the value of troubleshooting as a learning experience. However, a lot of people buy these kits so they can have a clock, not a learning experience! Thanks for being willing to play along here chasing down the problem.
Look into it later when the dust is clearing off the crater.
Given that my patch didn't solve the problem, if you're still willing I'd love to start over with a new board. I appreciate all the help from you and the others on this forum! Let me know what you need from me.