I started with compression testing each cylinder, each cylinder tested within the appropriate range and then replaced the spark plugs. Check engine light turned off and no more error code. Almost a week later the check engine light came back on and the rough idling at start-up started again. At that time I swapped the coil packs but still got an error code for misfire in cylinder 6. I called a mechanic friend, explained the problem and he thought it might be a bad fuel injector. That's when I posted my question about replacing the injector.
Before I got the chance to replace the injector I noticed white smoke coming from my exhaust pipe and it was lasting longer than it should and happening more often than it should. I checked my coolant overflow reservoir and it was almost empty. I went online, found out I was having the symptoms of a cracked head gasket (check engine light on, misfiring in cylinder 6, very rough idle lasting about 30 seconds after turning on engine, excessive white smoke coming from tail pipe, very low coolant reservoir) in a 4th generation 4Runner.
Between likely having a cracked head gasket and finding two shocks leaking in my X-REAS suspension, I decided to trade my 4Runner for a new Prius.