After installing the patches of doom, couldn't even start the game. So, I did a complete uninstall using Revo Uninstaller and CCleaner, plus searching through regedit.exe for anything remaining.
Installed S3 then patched it including 1.8, then WA including 2.3.
Installed Riverview, checked to see if it was working and it was doing fine.
Disabled Store mode in options, moved the two files EA created in downloads in case they were needed but after disabling store they weren't.
Put the rest of the Sims3packs that I had in the Download folder, including the ones from here, and installed them from the launcher all at once.
Everything is showing up fine including the free content from TSR (hope it's not infected with termites) and, so far, the game is not crashing.
I could be wrong but, I think the two odd files are created by the store that is now included in the launcher and after turning it off they were no longer needed. I have not installed the World Tool as some are saying it may also cause problems. Waiting until it gets out of Beta. As for new content that is just now being created, I have no idea if it will work.
Update: Asian Fusion, Regal Living, and a couple of others stopped showing up. Tried deleting cache files, reinstalling, etc. but to no good end. Some of the clothes stopped showing up and now list as not installed. I don't know why it did this unless it just now detected that they were, ahem, not legit. I'm uninstalling and reinstalling without the patch of the damned. Maybe "the Hero who runs this forum" will find a way. The mojo is with him.