I use a flathead screwdriver to take off stock lightbars by simply prying them out. It frees the lightbar by breaking the two plastic points below the base of the lightbar that bond it to the interior of the car. But because the screwdriver can gouge the paint on the top of the car, place the screwdriver so that any paint scratched in the process will be completely covered by the lightbar after it is placed back onto the roof.
Any good adhesive will hold the lightbar back into place. Super glue will give you a rock-solid, permanent bond, however if you want your lightbar to be removable in the future for any reason, use a silicone adhesive. If you use super glue, use only very small amounts and allow the lightbar to set and dry in a ventilated area.
To remove the clear window assembly, push up (assuming you're holding the car upside down) on the rear window so that you can get a flathead screwdriver up near the rivets holding the plastic to the car, and pry. The window assembly will break free. Once you realize how unlikely it is that the plastic will break, you'll be able to pry it off with more confidence and eventually might be able to pop out the window assemblies with just your bare hands.