Reworking the 273 Adjustable Rockers

here's the pickup/NPT pipes! looks worse in the pic than it does in person & I just tossed em on there today with no alignment just to take a pic. (1) my "drill bit photo" hole is drilled to 1/8. should I drill on thru into the shaft & if so should it be with valve closed? should I do anything to the adjuster screw side other than plug the side (outside) hole that Ma drilled for the inner adjuster screw hole? should I plug the shaft "side" hole that is 63 deg from bottom bananna grooves/hole?