I have build this focusser 3 times and working well. The capacitor is only neccessary if you connect the Arduino to an ASCOM driver.
However 100nF or up to 1µF is enough.
Did you check the focusser on a PC with N.I.N.A or something using the Moonlite Ascom driver and does it work?

On EKOS you should open the INDI window and select the correct USB interface. Otherwise it could be that the automatic port selection interferes with an other interface like EQMOD.

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