From my reading, it seems that those holes are usually slowly worn or melted into the intake tube, so there would not be any significant debris to be sucked into the engine.

What were the results of the compression test? If you had one or more valves stuck open, you'd get zero compression on that (those) cylinder(s).

How are the cap and rotor? You could have weak or intermittent spark at those cylinders. Also, did you check the condition and gap settings of the plugs? Are the wires worn or cracked? The miss under load could definitely be ignition; also, worn ingition components can be affected by temperature (symptoms change as the engine temp changes).