Chances are your 3TB drive needs converted from MBR to GPT.
Follow this guide - http://www.sevenforums.com/tutorials/26193-convert-mbr-disk-gpt-disk.html
As for the SSD this is normal. You will always be missing a few GB due to over-provisioning.
If Windows is installed to the SSD you shouldn't delete the System reserve partition. It holds the BCD and I doubt your system will boot without it. You might have to boot from a Windows DVD and run Startup Repair to fix this.