3TB WD Drive in EZ-Dock Formats to 801GB

Yes your right older products have a problem with bigger than 2TB drives. I sometime ago bought a Freecom Quattro dock which has USB2.0, FireWire400, FireWire800 and eSATA ports. This is perfect for your classic Mac Pro.

See http://www.freecom.com/product/hard-drive-dock-quattro-35296/

The first one of these I bought came with older firmware which could not handle drives bigger than 2TB however Freecom issued a free firmware update which enabled it to handle bigger drives and I have regularly used 4TB drives since with no problems.

If you buy a new one now it should come with the newer firmware already installed but if needed here is the updater.

See http://files.freecom.com/firmware/307174_HD-Dock-Quattro-Updater.zip

Unfortunately this updater needs to be run in Windows.

Note: On your model of Mac Pro FireWire800 is going to be the best choice. However if you want something more future proof and are prepared to pay more then have a look at this OWC Drive Dock: Thunderbolt 2 + USB3 Dual Drive Bay... at MacSales.com it has USB3 and Thunderbolt interfaces, you would not be able to use the Thunderbolt on your Mac Pro but could use either the built-in USB2.0 interfaces or get a USB3.0 or USB3.1 PCIe card for your Mac Pro and use that.

Open Disk Utility

select the drive by hardware-name

look at the reported information.

If the drive is reported as an 800-ish GB drive when you know full well it is a 3TB drive, you have the 'interface card in the enclosure is too old' problem, and how you format will NEVER get you beyond that reported size.

Old drive enclosures sometimes cannot accept drive larger than 2.2TB and would exhibit the symptoms you describe. That enclosure may work fine for smaller drives.