Like Tone mentioned, it would require modification, both floppy bays would likely be blocked by the vertical SIMMs.
You definitely want something with angled SIMM sockets. Even then - and especially with an '040 - you'll want to cut out part of the drive cage where the second floppy would sit, so there's room for mounting a heatsink/fan over the CPU.
I also agree with the above, the WarpEngine is a much better accelerator than an '040 MKII.
