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The upper intake plenum is leaking coolant into the cylinder heads. The head gaskets on this motor are awesome. So, chances are it's the upper intake plenum. You can check this, by removing the vacuum hose that runs between the upper plenum and the brake booster. Stick your finger in and try to touch the top of the lower intake manifold. If your finger is wet it the upper plenum. You might as well replace the lower intake gasket while you're performing this work because they are prone to failure also. Use a shop vac to pull any coolant out of the cylinder heads. Get brand new spark plugs because the old ones are probably fouled. Once you get the plenum and gaskets replaced, remove your fuel pump relay and leave the spark plugs out and turn the engine over repeatedly for about 10 seconds to push any excess coolant out of the cylinder heads. Then, put the spark plugs in and turn the engine over for 10 seconds again. This will burn excess fuel as coolant out. Then, replace the fuel pump relay to allow fuel to be pumped into the heads. Car will smoke for a few when it fires up, but will clear out quickly. CHANGE THE OIL! Twice within a week if possible.
alot of times the coil goes bad and kills the driver for the cylinder, remove the plug wire from that coil and see if it has spark if it does then my next step would be to do a compression test on #2 cylinder to make sure its not a mechainical problem. if the compression is good then check for vacuum leaks around that cylinders intake port and last is to make sure the firing order is right.the last thing would be to swap that injector with another cylinder and see if the misfire moves.good day.
I see a lot of lower intake gasket leaks on these but usually you get an external leak or you'll find coolant mixed with the oil, not a misfire. Upper plenum is dry on the 3.1 and just bolts onto the top of the lower intake. We usually apply pressure to the cooling system overnight with the spark plug removed from the misfiring cylinder. If there is coolant in the cylinder come morning then you only have to figure out where it is coming from. If the plenum is removed during the test you might be able to see where the coolant is or isn't coming from with a borescope by looking down the intake runner.
Usually the source of the leak is the gas cap (either loose or defective) but if that doesn't apply to your issue then the canister is next to the gas tank.
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