You should be fine storage wise, the issue is more that the 1,1 is SATA II where as new drives are SATA III. Still compatible, but will run at the slower speed.
As for your mac pro it can have 3tb hdds. Just like the newer ones can. Not sure if you can run 4 in a raid0 to go to a 12tb volume in an 06. the 10 model can do that.