If the flywheel groove is not perfectly inline with the wadeing plug hole, you need to slacken the three bolts that hold the IP locking plate in place, and move it such as the drill bit WILL fit in the hole WHEN the flywheel groove is dead central.
ie. remove the drill, move that tiny bit to make the groove in the flywheel central, then hold evreything but the ip in place (either with locking tools, or just get it in gear, and make sure nothings going to move) - THEN loosen the three bolts on the locking plate, and use a socket on the center nut of the pump to adjust it so as you can get the drill bit in place - then tighten up the three bolts again.
The locking plate gives a small amount of adjustment between the pump and the sprocket that drives it - it is designed to give this fine tuning.
Note -
The locking plate bolts are so very easy to round the heads on. Theres no clearance with the timing cover on to get anything else on them but sockets - so start with a good 6 point socket, (rather than a 12) and make sure they dont get rounded.