Not knowing the specifics of your project, it seems like that you are using USB to communicate with the Arduino. If this is the case, another approach would be to write the Arduino code to use the commands of a "serial" protocol such as LX200 or NexStar. This would make it compatible with any application that has the option to use that type of mount. (INDI, Stellarium, etc). From there, you could simply have a USB connection to the Arduino and select that type of mount in the EKOS guiding tab.
I have done a few projects which make the Arduino LX200 compatible and they have worked with both INDI and Stellarium. You can find the LX200 protocol on the Meade website.
Here is one that I wrote for an ST-4 to AutoStar (LX200) interface. I made this for an old Meade telescope that did not have an ST-4 port before I started using INDI/Ekos. (I used it with the GPIO ST-4 output of Lin_Guider.) It senses the state of 4 inputs and sends serial start/stop commands to the telescope handset serial port for guiding corrections in 4 directions.
There are actual pulse guiding commands in the LX200 protocol that I did not use here that you may want to look into for pulse guiding.
Although your project would probably convert the serial commands to Arduino outputs, the principle would be the same.