What year Sonata did your engine come out of?
There's a guy on here in Wy. that just put a Hyundai V6 in and he didn't metion having any problems with untapped holes.

dave h.
'89 Raider V6 5spd;Aisin Hubs;; Gen2 LS: frt. brakes, rear coils;U.C.arms;R.trailing arms;idler arm; rear LSD axle w.disc brakes ;2 battery system for Dog's fan; relocated ECU; custom bumpers;J.Baker receiver;Conferr roofrack; t-bar crank.