Hi Mateo,
1. You
don't need to connect JP1 and JP2. These are already connected on the top layer of the PCB. In fact none of the small headers on the board need connecting for the purchased PCBs.
The connector footprints are only there to allow people to home etch a single-sided version of the design.
2. For a standard ST-4 guider, pin 1 (IO0) is unused. This pin has a custom use on the AstroEQ to enable a push-button controlled mode to allow use of the AstroEQ without a PC for basic tracking an manual slews (see
here for details).
3. Correct, simply connecting the four ST-4 pins (RA+/- and DEC+/-) to ground will cause the telescope to change the tracking speed relative to the sidereal rate. The change is selected via the configuration utility. For example if you selected 0.25x in the config utility, then RA+ would track at 1.25x sidereal, RA- would track at 0.75x sidereal, neither would track at 1x. Pressing DEC+/- would cause the DEC axis to additionally slew at 0.25x sidereal while pressed.