It would appear that I got ahead of myself. I've tried deleting my .ini files and letting Enderal generate them again, I've tried using the set from the thread you linked (thanks for that by the way), and I've tried hybrid .ini files (blending those that you linked with the settings from the
S.T.E.P. Wiki since that's the modded version of Skyrim I previously had no issues with) and the mini freezes were always present.
While the freezes are like clockwork when they get started, it appears that they don't always start at the same time when I load the game. Deleting my old saves and starting a new game with fresh .ini files allowed me to get all the way through the beginning cut scenes before I started freezing in the level-up cell or the island (I don't exactly recall which). Replacing my .ini files with those that you linked allowed me to play for about 30m on the island before freezes began. Using the hybrid .ini files had me freezing after about 5m.
Honestly, I don't think it's my .ini files anymore; or if it is, it's a specific setting that's clashing with Enderal that didn't have issues with Skyrim. Another factor might be my hardware; since I couldn't find anyone else in the forums with this issue, there might be a conflict or deficiency with my PC and this mod.