Do you mean with the Java included with the SH3D installer, as Hansmex said would work fine?

Yes, otherwise I wouldn't bother to include it [;)]

Is all 3 of those directories/installs necessary?

No, in version 5.1, only jre1.8.0_60 directory is necessary. I should update the installer procedure to delete the old jre directories.

Would it be advantages for me to uninstall SH3D and reinstall the 5.1 version?

It's the safest way to remove the unnecessary directories.