The Problem: My 2013 Prius has a rough idle/engine shake and a Short Term Fuel Trim (STFT) of +18%. It is throwing a general misfire code along with specific codes for Cylinders 1 and 2. Work Already Completed: New Parts: Throttle body, ignition coils, and spark plugs. EGR System: Both the EGR valve and EGR cooler are new, clean, and recently replaced. Head Gasket: I have confirmed this is NOT a blown head gasket. The Theory: I suspect a high probability of air bubbles in the cooling system. I recently replaced several coolant hoses in the rear of the engine and believe air is trapped near the temperature sensors. The Plan: Vacuum Fill: I am performing a full vacuum-refill of the cooling system using a professional HVAC pump and refill kit to ensure it is 100% air-free. Smoke Test: If the vacuum fill doesn't drop the fuel trims, I’m moving straight to a smoke test to check for unmetered air/intake leaks. Question: Beyond the common intake manifold gasket, are there other specific spots on the Gen 3 intake or EVAP system where unmetered air leaks are common enough to cause an 18% trim?
You told us about the short-term fuel trim (STFT). What is the long-term fuel tirm (LTFT)? You add the STFT and the LTFT together to get the total fuel trim. As already mentioned, air in the engine coolant system will not cause misfires in the engine. There is a vacuum hose connected to the intake manifold near the throttle body. The hose runs over to the VSV valve. Also, there is a vacuum hose on the other side of the VSV valve that then connects to a steel tube near the EGR valve. Those two hoses are prone to cracking at the ends.
How did you confirm that? By chance with the syringe-of-liquid drawing up coolant test? That only tests for carbon monoxide in coolant, which is NOT the usual head gasket failure mode. What's the miles? First time cleaning the EGR?
Bad hoses is a good place to start... Also move around the ignition coils and see if misfire codes move to different cylinders. If the misfire codes were in cylinder #3 and #4 I'd be more in agreement that you've eliminated headgasket concern and its something else. But all the premature headgasket failures in Gen3 is a super tiny near microscopic coolant leak between Cylinder #1 and #2 and often takes years to go from symptoms of an occasional rough cold start to actual engine failure.
OP seems to have described a continuing misfire, not a cold-start one that quickly goes away. Head gasket thoughts might be a distraction here. STFT (should also look at LTFT as Brian mentions above) gives an impression that the ECM is trying very hard to get enough fuel in there. Could be bad fuel pump or clogged injectors preventing enough fuel delivery, or bad vacuum hoses admitting too much air.