That seems to have done the trick. I can quit safari and Cookie empties the cache without any problem.
The chown command changed

-rwxr-xr-x@ 1 ronaldgold  admin   47 Feb  7  2016 clearCookies.sh
-rwxr-xr-x@ 1 ronaldgold  admin  119 Nov 18 08:04 clearSafariCache.sh
-rwxr-xr-x@ 1 ronaldgold  admin  159 Feb  7  2016 clearSafariHistory.sh

to

-rwxr-xr-x@ 1 ronaldgold  staff   47 Nov 18 08:04 clearCookies.sh
-rwxr-xr-x@ 1 ronaldgold  staff  119 Nov 18 08:04 clearSafariCache.sh
-rwxr-xr-x@ 1 ronaldgold  staff  159 Nov 18 08:04 clearSafariHistory.sh

I spoke too soon. Less than 24 hours after reinstalling Cookie 5, Cookie once again gets stuck on clearSafariCache.sh. Any more suggestions?

Problem seems to be solved. I deleted Cookie Application and associated folders and files, rebooted computer, and reinstalled Cookie. I still have only three of the 5 scripts listed a being in the com.sweetpproductions.Cookie5 Folder, but clear safari cache no longer hangs.

Cookie 5.2.1 sticks at same point indefinitely. The output of scripts for me is:

-rwxr-xr-x@ 1 ronaldgold  admin   47 Feb  7  2016 clearCookies.sh
-rwxr-xr-x@ 1 ronaldgold  admin  119 Nov 18 08:04 clearSafariCache.sh
-rwxr-xr-x@ 1 ronaldgold  admin  159 Feb  7  2016 clearSafariHistory.sh

I seem to be lacking two of the scripts listed in your output and they are all assigned to admin. What next?

iMac (late 2013) MacOS 10.12.1