I have a different Yamaha receiver (RX-V373) and it allows me to adjust the relative volume of various inputs. You might check your receiver to see if it offers a similar feature.
On my receiver it's called "Volume Trim" and I can make volume adjustments for each input of +/- 6 dB. The Volume Trim settings are accessed via the "Option" menu on the RX-V373.
Adding 6 dB to the Phono volume, and reducing the volume of the tuner and CD by 6 dB might not get your playback volumes all the same, but it should help.