Time for a Mesa Card Upgrade.

ArcEye typed faster than me.

Rick G

microstepping is not for resolution , it's for nulling out resonance ,
you do not need high microstepping for a router , this is a falacy , and is the reason your having so much problem ,
it's also impossible to reach 0.0001 with a home built stepper machine , yes the numbers may dictate , but in reality it wont , and will not be needed in any case
back off the microstepping to half , and adjust your stepper values , slow the velocity down , and get the machine into the realistic ballpark , and correct first
and then look at where your at . it will be a far better machine if you do .

36v power power supply may be too low , for speed you would be better at around 60v , however it's possible the version of stepper drives you have , ditctate a dc input of 36v
so you'll be stuck their , and probably at a lower speed because of it . you'll need probably at least a 20A power supply too , as a guide .

you also have built the machine pretty heavy with 3/4 alu , so beware of having a high gantry weight ,
did you use self supporting rails ? .