The two M5 holes are for bolting this down to your extruder carriage (mine is a custom ORD-Bot carriage so you will almost certainly have to move these unless you want to get out the drill).

The countersunk M3 bolt holes are for attaching the front piece to the back piece after you've slipped in your j-head. These should be drilled out to 2.5mm and the bolts (I used 16mm length) will self-tap.

I would recommend drilling out the other M3 holes to 3mm. I think I didn't need to drill the M5.

The non-countersunk M3 holes are for bolting the mount to your nema17 motor. I also used these to secure a 40mm fan on the front to blow on the j-head (recommended for PLA).

I printed with support material to help with the lip for mounting the j-head.

Here is the hardware I used:
2 x (20mm M5 bolt + nut + 2 washers)
2 x (16mm M3 machine screw)
2 x (40mm M3 machine screws) these came with the qu-bd and are the right length for using their fan
2 x (20mm M3 machine screw) for securing bdring's thing:38281 to the motor
some M3 washers