Cliff,
I agree the problem may be a solder joint, but since 60m has great output and 40m is much lower, there seems to be something more. Also, I've tested continuity through all the LPFs, and all seems good.? Plus if the toroid joints were bad, I think the Nano VNA plots would have shown a problem.?
I'm suspecting something around L502 or T501 may be keeping the amplifiers from properly operating as Class E on the higher bands, or something like that. I will likely do some test with an O'scope later this week.
Walt