@everblue
If you don't have the flap, you can just use a suitably sized nut (see photo).
@Steve
I think the LED mounting screws are actually exactly the same as type #2, let me check again.
Edit: Yep, they're identical to #2 on this system, but surely slightly shorter would work too as long as the thread pitch is the same.
It should also be noted that since rev 1D.4 motherboards lack the rightmost part of the PCB (which has the mouse port) found on the other revisions, the mounting bracket for the floppy drive should be fixed slightly to the left (floppy drives do have a matching side hole there).
Accordingly, cases made for the 1D.4 motherboard (probably all the cases made by Amiga Technologies?) have the screw-hole equally moved to the left.