Hi Andreas,
At the moment this is not possible directly. Basically EQMOD does some initialisation of the AstroEQ controller when it connects, routines needed to get the motors to be enabled (sort of a safety feature by not allowing the motors to run when EQMOD is not connected).
I am looking at making the firmware automatically enable the mount in a stand-alone mode, but I haven't decided the best way to do it. Either it will enable (if not already) whenever it detects a pulse on the ST4 port, which will then allow tracking and guiding to be performed without EQMOD. This would be the simplest way, but phantom pulses on the ST4 port could enable the mount unintentionally. Alternatively, on all of the AstroEQ's since hardware V4.3 have a GPIO port on the PCB (5-pin header between the PIC and ATMega), these are currently unused, and I may make it so that a switch connected to this can select between standalone mode (serial port disabled, auto-initialise mount), and PC mode (serial port enabled, don't auto-initialise mount). I think the latter would be the cleanest way of doing it from a software perspective, though it would require soldering on a switch to this header which may not be for everyone. Your thoughts?
I am working on some firmware improvements at the moment, and will integrate the changes for standalone once I know which of the two routes to go down. ETA on the new firmware is sometime in early January, once I've had a chance to test and verify everything.
In the meantime, there is a work around. If you open up EQMOD using the "EQMODLoad.vbs" script (just double click on it) in the "/bin/" folder of the AstroEQ config utility. Once EQMOD has to connected to the mount, set it in to sidereal tracking, then run the "EQMODQuit.vbs" script. This will get EQMOD to initialise the mount. Once disconnected, the mount will still be enabled and tracking, and also allow guiding with the ST4 port, even if you disconnect the USB cable (as long as you don't turn of the power).