Drill the holes (in the bellhousing), grind them, whatever it take to get the bell housing centered. Then you weld these half circle guides on the bell housing over the locating holes while it's centered and tight on the engine. I had to do this on my hemi's bell housing. Pretty simple, mine was way off too. Most likely the bell housing itself is off (and maybe the block a bit) them things are jacked. I've milled a ton of the things just so the mounting face is parallel to the block. And it seems like the're rarely close to centered out of the box.
