Okay so after reinstalling El Capitan, my whole desktop was restored back to normal.
The only thing that seems to be left over is the number of partitions that I have. It seems as though there is still a partition that is not showing up in Disk Utility. I can see it in terminal though and it's the same size as my original bootcamp partition.
Disk Utility(it's not finished indexing, I'm guessing that's why it's showing so much "Other":

Output of diskutil list:
Niks-iMac:~ Nik$ diskutil list
/dev/disk0 (internal, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *121.3 GB disk0
1: EFI EFI 209.7 MB disk0s1
2: Apple_CoreStorage OSX-Macintosh-LVG 121.0 GB disk0s2
3: Apple_Boot Boot OS X 134.2 MB disk0s3
/dev/disk1 (internal, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *3.0 TB disk1
1: EFI EFI 209.7 MB disk1s1
2: Apple_CoreStorage OSX-Macintosh-LVG 3.0 TB disk1s2
3: Apple_Boot Boot OS X 650.0 MB disk1s3
/dev/disk2 (internal, virtual):
#: TYPE NAME SIZE IDENTIFIER
0: Apple_HFS Macintosh HD +3.1 TB disk2
Logical Volume on disk0s2, disk1s2
88C3D13E-0390-402B-B45C-C0D1B6756E3A
Unencrypted Fusion Drive
/dev/disk3 (external, physical):
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *5.0 TB disk3
1: EFI EFI 209.7 MB disk3s1
2: Apple_HFS Time Machine Backup ... 5.0 TB disk3s2