any idea how do i fix this problem ?

[doctorq]

You just have to buy a tower that has the right size. It should be easy to find a tower that can hold both A1200 motherboard and busboard, and also the cards you want to add later on.

You will most likely need to make a new backplate for the tower. If you don't want to do that you will have to do some research around the net to find out which Amiga towers were used with the busboard. I'm sure Micronik made one :-)

[doctorq]

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.