Yesterday I wanted to play the game again (didn't have much time for it for a while) but I got Script compilation errors. I deleted the two mods that were named and yet, when I now start the game, I get this:

Error [content0]game\actor.ws(3731): Function 'RemoveAllNonAutoEffects' does not take 2 param(s)

Warning [content0]engine\environment.ws(30): Global native function 'EnableDebugOverlayFilter' was not exported from C++ code.
Warning [content0]engine\environment.ws(32): Global native function 'EnableDebugPostProcess' was not exported from C++ code.
Warning [content0]engine\showflags.ws(11): Global native function 'DebugSetEShowFlag' was not exported from C++ code.

I tried the Script merger but the error remains

I even disabled all the remaining mods, yet that error remains. How do I find out what's causing it?

By removing ALL of your mods, including any binary libraries (dll etc.), verify/repair your game and then add the mods back in, one at a time to verify which one/s is causing the error.