First of all, that's a Mikronik case with a Mikronik zorro board, which is a no-go in itself. There have been a few different revisions of that Zorro daughterboard, and to my knowledge, none of them is a multilayer. As a result, all Mikronik Zorro boards make the system instable due to insufficient grounding, so I recommend to put the A4000D back into it's original case with it's original Zorro daughterboard.
Whatever you decide to do, you will need the A4000D version, because that's the motherboard you have. The special version's mechanical shape accounts for the nearby slot that carries the daughterboard, and it also accounts for jumpers that stand up fairly high from the motherboard. The highest spot of the 20-pin connector is 19.5mm above the mainboard, so clearance between the mainboard and your daughterboaard must be 20mm or more.
This is about the same dimension as the old unit, so if anyone here has a Mikronik daugherboard running with the A4000D version of the old design, he/she could maybe confirm that it fits (or not).