Those plugs are not in anyway connected to the coolant passages, they are oil passages from valve cover to valve cover. You will need a large allen head type socket. When you remove the #3 gasket, you can either replace it or use washers to seal them off. I think Napa carries the large brass washers. Or you can use Toyota FIPG or Honda Bond to seal them. The #3 gasket helps keep the debris from falling in the valley. Since I clean mine every so often, I decided not to replace the #3 gasket. So far no oil leak for over a year already.
As for your other problems, are you getting any engine codes? Also check your radiator cap, replace if you have not replace it yet. For missing, check your plugs, rotor and cap.
Good Luck!!
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