Okay, I noticed that JK does 'import' my old keys (the .plr file), only some of them (among which the Right Shift key) still do not work in game, even though they are correctly bound in the keyboard settings.
Another major questionmark though!
Today I was going to test my new level, and to my surprise I noticed in the level selection screen all kinds of levels showing up that I had actually deleted from my episode folder.
So I'm running a search on my HD to see where Windows/JK was keeping these files and it turned out there was a copy of my entire JK folder somewhere deep down in Application Data.
(C:\Users\Name\AppData\Local\VirtualStore\Program Files (x86)\Jedi Knight\)
Not everything was there though, the original JK level gobs were there, levels I had played after installing JK were there, but in my player folder there was only the file of the player I had been using (there are more player files in my original folder because I'm using a separate player file for each mod I play).
The JK exe wasn't there though, nor the jk_cd file in resource.
Why does JK/Windows do this? It's really annoying because now it seems like I have to manage 2 JK folders instead of one.
Can someone explain to me why this happens and what I need to be aware of in this regard?