Main mounting plate is 1mm thinner than motherboard mount points (spacers?), I've added several pads made out of 1mm polypropylene sheet on the bottom.
Fan mounts are made of acrylic scraps (left from previous work), each one has a tapped hole for attaching the fan:

All mounts were cut and sanded, exact fit was not necessary:

Fan mounts are glued to the main plate using epoxy glue, main plate was scratched in areas where mounts are touching it before epoxy was applied:

And the fan in place:

On the last picture you can see where I removed plastics from the fan before- just near the lowest mount. Otherwise I'd have to cut out more acrylic which would make the area less durable (initial fan outline is still visible).