If the issue involves your internal HDD: Try running Disk Cleanup, too. You have probably programs and files since you started using it. As the HDD gets filled with files, it takes longer to "find" empty space to write new files and it takes longer to "find" the files you want to open. Can you move some files to an external drive?
If the issue is transfers between the internal HDD to the external HDD, check the cable for nicks or other wear that may be causing the problem.