I have the same valve train noise and have found the same problem shifting between gears, especially when shifting from first to second. I spoke to the dealer about it and they said it is the nature of the beast. The dealer said the Thunderbird has a heavy duty clutch/transmission and they are all like that, I don´t know enough about it to know if they were just brushing me off or if they know what they are talking about.
Well my bike has been at the dealer a week now and they have only contacted me one time to let me know that they are waiting for some additional parts. They are going to replace my horn since they could not fix the problem with the original horn. I have not called the dealer since I do not want them to rush the repair work and not get it right this time. If I do not hear from them by COB tomorrow I will give them a call. I´ll let you know how it all turns out.