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When modeling everything, the connecting rod cap screws do come close to the engine block walls, but they do not touch. Differences in printing tolerances are most likely to be the problem as some people have had this problem while others have not. I experienced this with my first model but modified the connecting rod caps to allow for more clearance.

Some things that you might try.

If the 623zz bearing fits loosely in the connecting rod, try sanding the mating surface on the connecting rod cap.
If the bearing is tight, you can still sand the mating surface and re clearance the hole.

You can also drill a slight counter bore for the SHCS to recess it into the cap.

Your SHCS might also be too big, the head on mine measure 5.4mm in diameter and are 3mm tall.

You can also try metric hex head screws if you can find them.