I'm not sure about the first part, perhaps you could wait until you have test fitted the parts before you drill the dowel holes.
The four jacking screws are to support the gantry before you install the long pipes, like four table legs. You have to do this step before you install the bed support structure. You rest the gantry on the base support structure then lower the four screws down (effectively raising the gantry above the base support structure) adjust them until you are happy with the gantry's position - you could check it with a level. Then you install the pipes and raise the screws back up to allow the gantry to move.
These screws aren't essential if you need to use the space for something else - you could raise the gantry using wedges or something