I think it may be moving too fast, it takes just under 14 seconds for the RA stepper to rotate once when at sidereal speed, is this correct please?
The EQ5 mount has a 144:1 worm gear ratio for both axes. 360° / 144 = 2.5°, the angle of mount movement with one revolution of the shaft. If you are using the 40 and 15 tooth pulleys from the FAQ (with the 40 tooth pulley on the mount shaft), then 2.5° / 2.6666667 = ~0.9375°, the angle of mount movement with one revolution of the stepper.
Sidereal rate ≈ 1° / 4min. So it should take about
3 minutes and 45 seconds for a full stepper revolution at sidereal rate.
The default values of the EQ5-Custom-Pulley.conf are correct for this configuration, make sure you also have the correct Motor Driver IC selected (defaults to DRV882x).
As far as microstepping, it shouldn't make much difference regarding sidereal tracking, it's more about how fine the resolution of nudges can be while guiding. Ideally you want to use the highest number your Motor Driver IC supports and enable Gear Changing (these are the defaults).
What are the Voltage and Phase Current specifications for your steppers?
Are you using the AstroEQ with Windows/ASCOM or Linux/INDI?
Which version of the AstroEQ firmware are you using?