The mc18 Pulse coil connector will fit the mc16 loom, I've done it the other way (ie mc18 electrics onto an mc16). The '16 flywheel did not work with the '18 electrics (on the pgm2 setup anyway) due to the size of the 'trigger' area on the flywheel. The '16 has one about 1/2" long and the '18 has 2 smaller ones.
So I'd guess with the '16 flywheel, your mc18 will run with a '16 loom.
It would, as Andy states, be a step backwards though. Like putting '16 wheels on a '21. Or a '28 swingarm into anything else..
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More **** two strokes than you can shake a **** stick at.