Thank you guys for your help
So finally think I got it all straight, every time I think I had a consistent homing sequence, even without printing, later on in the day it would prove me wrong.
I finally settled on a very low current and a filtering of S3 in my M915 command in config.g
So here is my final configuration:
M569 P0 S1 ; Drive 0 goes forwards
M569 P1 S1 ; Drive 1 goes forwards
M569 P2 S1 ; Drive 2 goes forwards
M569 P3 S1 ; Drive 3 goes forwards
M350 X16 Y16 Z16 E16 I1 ; Configure microstepping with interpolation
M92 X160 Y160 Z403 E820 ; Set steps per mm
M566 X1000 Y1000 Z200 E900 ; Set maximum instantaneous speed changes (mm/min)
M203 X18000 Y18000 Z1800 E18000 ; Set maximum speeds (mm/min)
M201 X2200 Y2200 Z200 E3500 ; Set accelerations (mm/s^2)
M906 X1300 Y1300 Z1000 E700 I25 ; Set motor currents (mA) and motor idle factor in per cent
M84 S10 ; Set idle timeout
; Axis Limits
M208 X3 Y0 Z0 S1 ; Set axis minima
M208 X310 Y312 Z437 S0 ; Set axis maxima
M591 D0 P2 C"e0stop" S1 ; filament monitor connected to E0 endstop
M574 X1 Y1 S3 ; configure sensorless endstop for low XY
M915 X Y S3 F0 R0
M913 X20 Y20 ; reduce motor current to 20% to prevent belts slipping
G91 ; relative positioning
G1 H2 Z5 F4000 ; lift Z relative to current position
G1 H1 X-333 F4700 ; home X axis
G1 H1 Y-333 F4700 ; home Y axis
G1 X5 Y30 F4000 ; go back a few mm
G30 ; home Z by probing the bed
M913 X100 Y100
I also removed all M915 commands from both my start and end slicer gcode config. I was playing around with stall detection and forgot I had some M915 commands in there.
So I'm still not sure why I need such low current in my homing files, but I have tested this about 100 times, after a fresh power-up, both hot and cold, and printing 25 models back to back.
I'm still mapping E1 to Y axis, but I'll probably revert that back to normal after a few more days of testing.
DC42 - yes, after a print job when it would park the nozzle in the far right corner, on the next homing sequence it would trigger X as stalled and move only the Y axis.
I'll play around with your suggestions, but at this point I am satisfied and all seems to be working well.
I still find it VERY odd that moving the homing current above 20% will not trigger a stall, but instead make the Y axis motor spin in the wrong direction, but that does not happen during normal printing.. I don't understand how/why that happens..