I had the same problem. Loads of ways to do it I'm sure, but I found paper templates were the easiest, especially since I had a weird little angle that needed jigsawing out too.
After measuring lots of things and getting it wrong every time I just pressed the part against some paper to make a paper template, cut it out and just drew on it until I was happy with the placement. I marked the center of the drill? motor plus a larger circle showing where the rest of the motor would sit. Then I just taped the paper template back onto the part and drilled through it.
If you have some decent clamps you can clamp both sides together and drill the pilot hole through both sides at the same time so they will be an exact match.
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