Wow lighting is really hard, or maybe I just suck at it. Surprizingly there sre very few good tutorials on lighting. Is there a way to reset all sectors back to fully lit in JED? I really just want to start again, but just on the lighting.

If I remember right, you can only set the lighting back to full for the preview window. The easiest way to do lighting is to split everything up into layers and hide the ones you don't want to light yet. Then just select the visible sectors and calculate lights in selected sectors. When you have the lighting the way you want it, deselect the sectors and hide the layer. Repeat for each area.

Load a .jed file prior to your lighting attempts (don't tell me you have none...just don't). Lighting is a bit screwy in Jedi Knight, as there are no lightmaps (like in Quake3, e.g.). There is only vertex-based lighting (check out the lighter plugin) and dynamic lighting (use things that spend light). Both methods need a lot of tweaking for special architecture. And sometimes it's just impossible to make it look good.

if you don't have a backup "level".jed file, you could try renaming the "level".~je to "level".jed.

It might be a backup from before lighting.