After making sure that my saves would be safe (in My Documents), I ended up fully uninstalling Enderal, and then fully uninstalled Skyrim. I also deleted any ini related to Skyrim in My Documents, keeping nothing except my Enderal saves.
Afterward, I force-checked my Enderalinstallation file in my torrent client to make sure it contained no errors (it doesn't, it's fine). I installed Skyrim, didn't touch it or launch it, and then installed Enderal. Also patched it through the launcher.
The Enderal Launcher doesn't give me error messages anymore, but the SKSE issue remains.
I still get the Memory Fix error message unless I create a shortcut of SKSE_Loader and add -forcesteamloader at the end of the Target address. Doing that removes the message.