There's no partial WD EARS alignment fix:

I had data on /dev/sda3 and /dev/sdb3 (RAID1) so I couldn't edit that one.
I thought I'd be smart and try fixing the first two partitions so I set the first one starting at sector 2048 and then +8 for the second partition.
This has really slowed the performance down worse than it ever was!

Disk /dev/sda: 2000.4 GB, 2000398934016 bytes
255 heads, 63 sectors/track, 243201 cylinders, total 3907029168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x00000000

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1            2048    29362176    14680064+  83  Linux
/dev/sda2        29362184   146528864    58583340+  83  Linux
/dev/sda3       146528865  3907024064  1880247600   83  Linux
 

I wonder if by having two aligned partitions and my third being unaligned has thrown off performance on all partitions?  It doesn't make sense if that's the case.