Went ahead and increased R52 to 3.92K. Pretty much the same. Highest E, now comes as Eb +37cents, 5.29V. Highest C is 5.96V.
Then 10K, Highest E, comes as E +34cents, 5.36V. Highest C is 6.03V.
Then installed a 10K trimpot and seems it is fixed now! I can get the keyboard to tune correctly! I'm not sure if I should remove it, mesure it and replace it with a resistor of the same value. It is working now, so why bother?
I'll keep testing, watching the tuning and report back if any more problems arise.
Thank you very much, Florian!