If the piece is larger than your table how do you plan on clamping it down? Or is it just longer than the table with space for clamps on the sides.
To give yourself some reference points for re-alignment after doing one set of holes and moving the plate you could drill some pieces of flat bar to attach to the holes you have tapped. With the flat bar bolted on before you do the first move, machine a straight edge along the flat bar and interpolate a hole in it. The straight edge gives you alignment, and the hole gives you a position reference.
An open mind is a virtue...so long as all the common sense has not leaked out.