OK, nevermind, I finally found it.
I renamed both the compass and clock.xml files, to bring up the standard ones. Then I noticed that the standard ones appeared briefly at boot up in the bottom right corner of the screen, then the compass moved up and the clock disappeared. But, with I hovered the mouse over a small blank area in the bottom right corner, the clock pop up appeared. Now I finally knew where to set Window Settings for the clock window, turned all it's opacities back on, and moved it to the middle of the screen.
Then I renamed the compass and clock.xml back in to Profit versions, and restarted. Now I have the Profit compass with the Profit clock on top of it (default locations for both). I can even bring up the timer window by clicking on the clock now!