If the 4k alignment of your hard disk is off, there are ways to correct it. A number of utilities exist to do this. A good (and free!) program is the MiniTool Partition Wizard Home Edition that you can download from www.partitionwizard.com.
Once you've installed it and got it up and running, it will show you an overview the disks and partitions on your system. If you need to align anything, you just click Align All Partitions. The software first checks whether alignment is necessary. If so, the Partition Wizard indicates which partitions will be adjusted. Click Apply to get it started. It will restart the computer, as partitions can only be adjusted when Windows isn't running.
How long it takes depends on the size and speed of your hard disk. When it's finished, the hard disk should be faster.
The MiniTool Partition Wizard can align all your partitions.