That seal MUST have a special sealer on it. You can use 3M 847, which is the BRP brand, and the easiest to use. clean surfaces well with acetone, mate surfaces, then use the dowels to bring them together. Then torque all bolts to spec. You will get an air leak, which is what you now have, and will run lean, and leak fuel/oil mix out.
BTW, the fact that you were getting continuity from either coil ground to one of the spark plug leads is totally normal.