I just studied the pics from my stock 216 when I pulled the head and it too had 2 holes in the head but no matching holes in the block. The old headgasket had holes in those positions as did the new head gasket but again, there are two holes in the head but no matching holes in the block.
Based on the crud that was built up those holes in the head are in the water jacket.
I'm the 2nd owner of the 49 3100 and to my knowledge the engine was 100% original (bareing normal wear & tear parts).
The built up crud in your head could be your issue but the two blocked off holes in the head probably are not the issue unless that was a major change between the 216 & 235 blocks.
Good luck
Dave.
