One amp I’ve owned and don’t usually recommend to everyone is the VPI 299D, but it fits your search perfectly. It is more refined than other tube integrateds from Rogue or Primaluna and has a MM phono built in.
It was designed in joint by Harry Weisfeld (VPI) and Steve Leung (of VAS audio). Only 100 of them were made. One is on USAM now, and I have no affiliation with the seller:
The tube rolling is as extensive as a Primaluna, but has the added tube rectifier which can accept GZ34/5R4/274B variants. It lets out a lovely sound and will be bolder than your Yamaha (I’ve owned an A-S3000).