Installing a 3Tb drive requires a special adapter from WD. This not something to ignore or bypass, it should be explained in the docs, if you didn't get the whole kit. If you got non-kit supplied 3Tb drive, then you need that adapter to fully be installable. In your case, you already have an adapter to supply SATA ports, but does it support 3Tb drives. Thus, it can get complicated real fast. However, it can be in "addition" to other ports using the WD supplied adapter.
Shuttle SN68PTG6 DELUXE AMD 6400+, 4GB, WD SATA III 600GB HD
Want to add:
WD 3TB SATA II HD and LG SATA 24X CD/DVD Burner
Is there a SATA controller with at least 3 ports that I can put all these on one PCI-E x16 slot
Will not be using RAID and have no FD.