This is what I would do ...but I'm sure other guys have different thoughts:
1) Double-check your battery connections AND esp engine ground/s. Sounds stupid, but engine electrical signals go through the grounds and a bad ground can spoof lots of crazy things. Esp on a 2011 ..which has some age on it and connections could be less than good. And it only takes a couple minutes to cross off the list.
2) Check the PVC and it's piping ..and vacuum hoses. Again this sounds stupid, but I've personally had it where plastic PVC piping and cracked rubber 90 degree elbows weren't sealing well. Such a problem can 'spoof' crazy unrelated problems ...even though you wouldn't think so.
3) Tripple-check injector and coil wiring & connectors.
4) Ohm out the coil packs 1-2 and compare to what the readings should be (sorry, I don't remember off hand). Warm the engine and remove the spark plugs at each of those cylinders and ohm them out too. I say ..warm the engine b/c if you don't find anything, I'd pull the rest of the plugs and do a compression test.
5) Perform a compression test by removing a plug from each cylinder. Test all cylinders (4 or 5 puffs each cylinder) ....and write down/compare the results. This won't catch a bad cam, but any misfire could be due to a bent/bad valve or head gasket issue. It's just good basic troubleshooting ...esp since you already have plugs from cyl 1&2 alread out. Otherwise if you don't do it and keep looking ...you never know and could waste a lot of time if it was a valve issue.
6) Observe the color and quality of the spark plug ends (for wear/cracked porcelean electrodes, etc). Ohm them out too. I've had internally failed spark plugs before. I'd replace them if they're old, or at least the cylinders showing misfire.
7) You could swap coil packs. Write down and compare readings.
8) If you haven't found anything by now, remove the valve covers on each side (or crank engine over) and observe the action of the rocker arms. You might find one not moving very much which means he's got a bad (worn) cam. Hopefully that won't be the case.
Good luck. Let us know what you find