Sorry if some of the information shared is overly simplistic or basic, but we don't have a way to know a person's background, and even those with strong backgrounds don't know everything, and even the best of us misses the obvious from time to time :) The 2TB limit applies to physical disks.  There is no limit on the size of virtual disks - at least not that can be reached within the capacity of the 2900 chassis.  Where in the 2900's manual does it give a 2TB limit?  Virtual Disks on the SAS 5/iR are limited to 2TB, but the SAS 6/iR and PERC 5/6/7/8 are not. Although the PERC firmware release notes do not indicate support being added in any particular version, I seem to remember that larger drives were not properly supported in the earliest firmware versions of the PERC 5.  None of the release notes indicate specific fixes or support added, but version 5.2.1.0067 (one newer than your current version) does add code to "improve CHS (Cylinder/Head/Sector) to LBA (Logical Block Address) translation" ... possible that allows a broader range of drives and configurations to work without issue. I would start by making sure your system firmware is up to date (BIOS, ESM/BMC, PERC, and the backplane firmware), then try your 1TB disks again, as there is no reason at that point (short of the possibility of an incompatibility with non-certified drives) that you shouldn't be able to configure an array greater than 2TB. 
 What I am looking for is information on what storage increase one might gain by doing the Firmware update on a PERC 5/i from 5.1.1-0040 to 5.2.2-0072? I found 1 white paper that addressed some of the advantages of applying the update but none that explained if the firmware allowed any storage increase from the 2 GB limit.   Thank you
Dell 2900 with PERC 5/i Firmware update to 5.2.2-0072