It can be done indeed saw various ppl who done it.
Friends of mine had an 603e 210Mhz with 040/25+bvision in the A1200
desktop, and even when de cooling fan died it still just kept working.
Now they have an 060/50+603e 240Mhz+scsiII+bvision in the A1200
desktop and it also works fine.
keep the trapdoor open and make sure there is plenty space (>2 CM),
between the miggy and the desk, and it will work just fine.
And modify a PC AT PSU since the original will not do by far.
Towering your A1200 would make much more sense since you also can get
access to Zorro/PCI expansion boards
My PPC A1200 is nicely towered in an elbox power tower with a Zorro
IV+mediator ZIV,bvision and lots more :-D
Btw i had an Apollo 040/40 about 3 years ago in my A1200 when it was
still a desktop and it worked fine with the trapdoor closed, but a
small cooler on the 040/40 cpu is a must in that case.
