Safari extremely slow and clunky after installing El Capitan

Reinstall El Capitan Without Erasing the Drive

Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears.

Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.

When the recovery menu appears select Disk Utility and press the Continue button. After Disk Utility loads select the indented Macintosh HD entry from the the left side list. Click on the First Aid button in the toolbar. Wait until the operation completes, then quit Disk Utility and return to the main menu.

Reinstall OS X: Select Reinstall OS X and click on the Continue button.

Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless and more reliable.

Try a restart.

Do a backup, using either Time Machine or a cloning program, to ensure files/data can be recovered. Two backups are better than one.

Try setting up another admin user account to see if the same problem continues. If Back-to-My Mac is selected in System Preferences, the Guest account will not work. The intent is to see if it is specific to one account or a system wide problem. This account can be deleted later.

Isolating an issue by using another user account

If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer. For each disable/delete, you will need to restart if you don't do them all at once.

Safe Mode - About El Capitan

Safe Mode Startup – El Capitan.