Installing a BVision inside a A1200D worked really well for me. Although I have a 060 instead of an 040. (040 produces more heat). I also added extra fans inside the case. SCSI works well still 2. But I must admitt that I'm not using the 3D chip alot. ) I can play wipeout though without any crashes. Somewere on my HD I've got pictures of the process and the things I did extra. (Like extra ground wires and stuff) It all fits very well. Although I do use a 2" HD.
If you want to go for it, you should find someone using a 040 if it all works well. Be carefull !!
Cheers