There should be 6 holes (3 on each side) to bolt down the hard top. You're saying 4 were drilled out and 2 are not?? Look carefully where the un-drilled holes are supposed to be. There may be pre-marked punch points in the tub to guide you on where to drill them out. If not, mount the hard top, use a transfer punch to mark the holes, remove hard top, punch with standard punch, and step drill out to same ID as the holes in the hard top.