Ask them to define "upgraded" for the caps. Sounds like a ripoff to me.
Where did they put the 6 transistors in a tube amp?
Hum is usually due to bias mismatch between push-pull pairs in a channel, or there needs to be some hum balancing circuitry installed. Either way, I don't see ANY need to spend $1,000, especially if it is slight...
I'd suggest sending it to Rogue next time.