Before you start drilling things-- Years ago,I had a 65 Impala convertible, original 327 with a 3 speed stick. I decided to put a 340 horse 409 I acquired in it, and run a Muncie 4 speed. I parted out an absolute dog of a parts car, so the stuff I got off of it was year correct. On a 64 on back 409 car, the clutch pivot ball attached to the block on the side in front of the oil filter. Small block, same place. On the '65, however, the clutch linkage and the Z bar with the pivot bar were much closer to the firewall,and the pivot ball screwed into a threaded hole on the side of the bell housing. The hole was 7/16" NC thread if memory serves me right( it has been almost 40 years since I did this swap), but 65 was the year of the big change over on the Impala,and the Chevelle was a new car line just a few years previously.Without one in front of me to look at, I would guess that is the issue. The reason the bolt hole on the Mark IV motor isn't right is that that motor line up never came in a '63 Chevy. The factory would have had no use for it. If you are trying to put the 409 bell housing on the big block, it probably would fit the engine OK, but it probably wouldn't have the bolt hole either. I had to find a 65 396 bell housing to do my swap years ago, the 327 had the small flywheel, and the SBC 65 bell housing wouldn't go around the 14 inch 409 flywheel.