Why does my 2005 Toyota 4Runner shake?

Hello, if you have diagnostic trouble codes that are related to cylinder misfires and you have done "basic" repairs of replacing spark plugs and coils, then further testing must be performed. You will need to find out if your cylinder misfire is related to an unresolved spark / ignition issue, a fuel delivery issue or even a base engine issue. Diagnostic test equipment can monitor spark at the cylinders. Further, a manual compression test may be a good idea -- see where all 6 cylinders are rating and see if the two cylinders in question are much lower than the rest in pressure. If so, a leak down test should then be performed. It is time to get "hands on" with testing, and stop researching to formulate guesses as to why the problem occurs. Testing will get you the answers you need.