I had to reset everything including all my hot keys.
As Neeno already pointed out, it is
important to move your setting files (like controls.cfg) and logs after having applied the mods and launched psextended for the first time. You will notice user data folders per character, and you can just dump your old files accordingly. Yes, that part seems annoying, but separate files per character can be nice to have.
[...] I seem to have a little more lag [...] and I can get through the load zones much better.
This can be a result of having (re-)moved the shadercache. Actually, I find myself deleting said cache file frequently to speed up my loading times, which does not really make sense, but turns out to work well.
Venalan: Thanks for your support