1. If the floor is solid build the wall on top of it. Can't really give a good answer to this Q as we can't see how the existing wood floor is constructed.
2. I installed my carpet directly on the concrete floor. I used an 8-lb pad under it. But I didn't have any water seeping thru. If there is water (moisture) then you're better off putting down a vapor barrier then a subfloor. If not sure try the moisture test - tape down a 3'x3' plastic on the concrete. Come back in a few days. If there's moisture between the palstic and concrete, you have moisture to deal with.
3. The pots lights will be no problem. If you are really concerend, get the IC rated pots.
4. Do use a vapor barrier on the walls.
5. You could build in a fake window. Just install a simialr window, having the wall behind it white. A fluorescent light above it (out of sight) and curtains in front and you can't tell it is non-functional.