There is no perfect case, that will solve your problem, because the holes for installing the Amiga 1200 and the busboard won't match. Therefore you should just buy whatever case you fancy and make a new back plate for it.
As for how tall the case must be, then it's a matter of measuring. You know you will need to have the motherboard in there, and you should also make room for an accelerator.
If you are planning on using ethernet cards through the PCMCIA port you have to take this into consideration as well. I'm not sure that, even if you buy a 45 degree adaptor for the PCMCIA port, you will be able to install a ethernet nic there.