Update on the morning exhaust backfire problem. The bike is still backfiring in the morning, even with the petcock closed.
I've noticed that the Pingle gasket has started leaking. I followed the instructions carefully, and after 3000km I thought that I wasn't going to have a problem. The gasket material included with the Pingle seems to be getting soft. I'll have to chase down the pingle leak threads and deal with this.
This is the only symptom that is coinciding with this new backfire problem. But I sure don't know how the tank gasket leak causes the petcock to leak fuel through to the carb to cause backfiring.