Had the same problem with the driver's side rear when I changed plugs a few weeks ago. Even when rotated the plug boot has to go in at an angle so it would miss the top of the plug. Bending the boot with your finger to guide it to the plug is the way to go but it's tight cramming your hand down there to get at it.
Any time you reset the ECU, which a battery disconnect will do, it takes a few seconds to "reboot" the first time it's powered up. Turning the ignition to just the On position and waiting a couple seconds (letting the gauge sweep complete is long enough) before starting is all it needs. If you don't, it just cranks for a while but will eventually fire up.