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Well you have went from an older single cylinder, to a newer twin cyl. engine. The older engines used a "trigger unit" that had replaced the old points/cond. system.
The newer engine should just have one wire to each coil for the "kill" circuit only, and that one should be wired into the "Kill circuit" on your old mower...
You need to be carefull, as mis-wiring these parts can destroy expensive parts. So I am not real comfortable on going on much further, as those coils are pricey.
It might be wiser to take it to a local shop that knows what they are doing, as they will have the benefit of having the mower in front of them.
Also, most newer engines have pesky wires going to carbs which further muddy up the engine swap.