SKSE's clear function can only do so much. If you have installed/uninstalled a bunch of script-based mods (or even non-script mods actually), you can expect some issues in your save file, especially after 2 years.
How big is that save? Also, enable Papyrus logging, play until you get a CTD, and skim through the log. You'll see just how much is left over in your save :)