Although I haven't tried it (don't have a 3TB disk laying around) I think 3TB won't work, no matter which firmware you load on the disk. The problem is the bootloader (uBoot). As you may know, uBoot has to load the kernel from sda6, and then it starts the kernel with the communication that it can find it's rootfs on sda7.
So uBoot has to be able to find sda6, and the kernel has to be able to find sda7. The classic MBR partition table cannot handle partitions bigger than 2TiB (2^32 sectors), so a different partition table is used, GPT
. uBoot has support for GPT since september 2008
, while the first wiki entry about the edmini v2 is dated januari 2008
. So the edmini v2 bootloader will not be able to find sda6.
*Maybe* you can create a mixed MBR/GPT partition table, but then still I don't know if uBoot won't be confused about the number of sectors. The only real solution is flashing a new bootloader.
So I think you should stay below the 2TiB limit. AFAIK the original Lacie kernel can handle that fine.
The 4k problem is no real problem. When you install the firmware just make sure you create aligned partitions for sda5, sda8,sda9 and sda2. If you fail to do so, the system will still work, but maybe a bit slower (although I don't think you will notice, the edmini is just too slow to suffer from the slower disk throughput.)