I need some help/suggestions with hesitations and misfires. I’m working on a 2009 Honda Civic (R18A1 1.8L) that experienced overheating and misfires on 3 of 4 cylinders. The initial tests I performed were:

• Compression test: good compression on all cylinders with little variance
• Leak down test: No leakage
• Checked for vacuum leaks, couldn’t find any.

The initial repairs made were:

• New Ignition Coils for all cylinders
• New spark plugs for all cylinders
• Flushed the coolant system and replaced with new coolant
• New Thermostat

After this, I was still getting misfire codes (P03XX). When I disconnected the Exhaust Gas Recirculation (EGR) valve and cleared the codes, they didn’t return. So, I replaced the:

• EGR valve
• Engine Coolant Temperature (ECT) Sensor

There are still periodic, brief hesitations (dip in RPMs) while idling. The hesitations seem to get more frequent after driving for a while. On one drive, the check engine light came back on and threw P03XX misfire codes on a couple of cylinders. I pulled the ignition coil wires on the affected cylinders, put them back on, cleared the codes and was able to drive home without anymore issues (other than the hesitations).
At this point, I have no idea what to do next. Any suggestions or guidance would be greatly appreciated.