Just realized CD DIRECT does not bypass this so maybe that's where I should start?
I'd have to have a look at the schematic later, but the 300/301/500/501 and 700/701 are all extremely similar apart from a CD direct buffer stage and IIRC another buffer stage to account for the losses in the digital vol/source selector IC.
The easiest was to determine where the problem is, is to start immediately after the source selection, where the signal is sent out of the main IC and then returns, gets looped into the dig-attenuator and then sent back out again. Look at the waveforms for each channel when fed a mono signal. They should be identical or very close. Then progressively go through the stages, comparing amplitudes for each channel.
Or, simply combine the L+R signals right at the power amp input (there's a L/G/R connector on the main amp PCB near the front) and check to see if it's balanced at the speaker terminals. That will rule out the power amp stage balance in one go.
Bear in mind, the volume pot is not traditional at all. Yes it's a two gang pot, but only one wiper/track is used to generate a voltage read by the A/D in the micro, which in turn feeds the digitally controlled volume IC. So you can't probe the volume pot terminals like a normal old school amp.
Put it this way, the implementation Yamaha uses provides perfect channel balance and particularly L/R tracking over the full range, so a mis-balanced unit means there is a problem.