This is what a knucklehead that has been converted to run pan head cylinders looks like. This was a popular deal back in the seventies. Chopper guys and girls used to have a hard time finding low bore knuckle cylinders, so they would use pan headcylinders. Four of the bolt holes in pan head cylinders are the same as a knucklehead, but one of them is in a different spot, so they would screw a head bolt into the hole, and drill and tap a different one.
The first step in changing the heads back to stock is drilling out the head bolt hole.
Then you put a bolt in the hole that was previously used for the pan cylinders.
Next step is to drill hole for the knuckle head bolt pattern, then tap it for a helicoil.
Here is the almost finished product. we still have to face the head bolt surface, but you get the idea. This is a good fix and will last a long time.