I keep forgetting to use the SimPE scanner.

I use the Clean Installer that you can get from MTS, which lets you delete after you find things that need to go away. I rather thought that SimPE had a delete, or at least a move function, but I might be wrong. I couldn't tell you where it is, anyway. You could try running the clean installer, then finding the files and deleting them there.

It lists them by the in-game descriptions rather than package names, so some of the bad packages would probably still need to be tracked down manually, but it does mark files that are empty, duplicates, etc. in pink, and ones that affect game code in red. (So don't dispose of all the red files or you will lose all your hacks. )

(As a side effect, most of those walls, floors, terrain paints, meshes, and recolors that have "alphabet soup" names get identified.)