Well, this will get long...
I need more details. Is this on a very small SD card? Is the SD card properly formatted? You can check the SD card in the Windows command prompt via chkdsk.
Well, once that is stable, once I know how it works, of course. In the meantime, helpful hints are appreciated.
Alright, still not sure if I got that right
. You can only do a Nintendo (home menu) System Transfer once the NAND is already set up, but that is not what you mean, right? So, you transfered the backup from 3DS-A to 3DS-B? For all that I know right now, that should not work at all. The first barrier would be the different encryption (fixable), but that is not everything that stands in the way.
Well, the EmuNAND size is decided the same way everyone else does it now (CakesFW, rxTools, ... even GW). EmuNAND9 is different from GW in that GW just decides to use a big chunk of your SD card (big enough to handle any size), while EmuNAND9 chooses the size based on the actual flash memory size. The EmuNAND created by EmuNAND9 should still be exportable by any other tool. Could you specifiy or give an example?
By the way, while the flash memory sizes differ, the actual NAND size does not. EmuNAND / SysNAND backups can easily be fixed to work on any flash memory size by truncating / padding. I could even build this right into EmuNAND9 (and yes, we could even save more memory). I need more details, though.
No, for SysNAND you need direct and full access to the NAND for this to work. This (access to SysNAND) is actually the only reason why EmuNAND9 needs ARM9 access.
No. You might be able to take over some stuff, tough, once you have set up your N3DS EmuNAND. I suggest you do a new thread for this.