How are your HDDs holding up? What is your daily throughput for these HDDs?
I just purchased two WD60EFRX 6TB (Red) for one of my DNS-345, which is essentially the same as the DNS-325 save the extra two bays. I've read a number of user reviews stating that these new HDDs have a rather high failure rate (either DOA or failing within weeks after purchase). For new purchasers, I suggest performing some heavy burn-in for the first month or so to make sure the HDDs are working properly. My intention is to schedule full backups across both HDDs multiple times per day for a month to properly burn-in the new HDDs. I'm also going to stream a BD movie on a repeating loop for a few days to tax the HDDs a bit.
Regarding the setup issues you've had, my intention is to configure these HDDs as Standard Volumes, so I don't foresee any challenges.
Not that this is an issue for the DNS-325 (yet), but I believe the Linux filesystem used on the ShareCenter has a maximum Volume size cap of 16TB. While this is not currently an issue for the DNS-325, it means that four 6TB Reds can't be used to make a 24TB JBOD or RAID-5 array on the DNS-345. Hitachi recently released an 8TB He HDD, which will prove interesting once the prices come down to something approaching reasonableness.