Hi there,
I know this is an old thread, but I couldn't resist my urge to throw in my thoughts on this one.
What you have to keep in mind about the Emu68 is... it's not just a piece of software that runs on the CPU - it IS the "CPU"; thus, without it, the computer won't run at all (unless it's installed alongside a stock CPU with, say, a Lazarustorm, of course).
The PiStorm doesn't use the SD card as emulated Amiga FS hard drives only, it has a FAT32 partition from which it loads the Emu68 kernel initially. Without this, there's no CPU and hence, no booting - not even from floppy. I've yet to read the OP's first thread; however, I know the above to be true.