I'm very aware that I'm a newbie here and I should probably enter the forum a bit more gently but I have a problem I could really do with some help with and it's a biggie.
I'm having an absolute nightmare trying to debug my new machine, I've been at it for seven days straight and I'm losing the will to live.

It's a pretty standard 8x4' setup.
2.2Kw spindle with VFD.
SM 86HT115 Steppers on Y axis with DM860e controllers on 48v.
SM 60STH100 on X axis with DM542 on 36v.
SM 57STH76 on Z axis with DM452 on 36v.
Generic Mach 3 controller board.

My right side Y axis is continuously losing steps no matter what I do, up to 2-4mm over the course of running for 20mins or so at between 45 and 70mm/sec.
I'm running two separate inputs for the Y axis motors.
So far I have checked all motor tuning is correct.
Checked the test tool paths I'm using are correct.
Replaced the controller board for another one.
Swapped over the two motor controllers, fault stays on the right motor.
Physically swapped over the two motors, fault stays on right.
Checked the rack pitch on both sides was identical.
Checked shielding on everything is properly earthed to the chassis.
Twisted the motor controller power supply wires.
Tried multiple PCs, fault stays on the right.
Ran the machine with the spindle off, fault stays on the right.
Ran the machine with the X axis powered down, fault stays on the right.

The only thing I've just noticed is one of the cables on the two Y axis motors is a different make to the other so I'll sort that out on Monday.
I've also been told that resonance in the body of the machine could be the problem but I've no idea what to do about that.
Feels like I'm clutching at straws now.