Bizzare behavior-Settings remain after app deletions

My problem seemed to begin a few weeks ago when the SuperDuper script wouldn’t run overnight. After contacting them, I ran Cocktail, deleting logs, caches, repairing permissions, and rebuilding the launch services database. Then I uninstalled recent apps: HyperDock, TotalFinder, and a haxie, WindowShade X.
More or less took care of that problem, but now a new and bizarre problem has sprung up. Despite deleting WindowShade (and the others using CleanApp), its behaviors remained. For example double-clicking a title bar rolls it up, which only WS can do. I tried setting my Logitech Control Center(yes, I know-it s#*ks) settings for the diNovo Mac Edition keyboard to use standard function keys, but pressing a function key opens the app I assigned in LCC prior to that.
I have a feeling that the problem has something to do with LCC, as recently the Logitech Revolution MX wireless mouse only works when the receiver dongle is plugged into ONE USB port only-top port on the front of my Mac Pro. Tried it with a spare mouse and receiver, and get the same behavior.
Is there anything short of a complete erase/reinstall of 10.6/update that I have overlooked? If I have to go that route is there anything I can migrate over that is safe other than network settings and applications. I’m afraid the problem is in my User folder and am leery of that. Thanks for any advice.
By the way, I do have a Time Machine disk, but have had poor luck when trying to roll back something in /Users/Library in the past.

After posting I did exactly that. Downloaded the installer for both (I had uninstalled APE earlier) then ran uninstall even though both were gone from SysPrefs. Solved both the WS and LCC problems. I'll certainly miss it. Thanks for the suggestion in case I hadn't come across it.

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