You should probably pull your toilet and turn it upside down to get the pen out, it's probably caught in the internal trap of the toilet and is lodged in there. If it's not in the internal trap then the snake can be inserted into the drain line once the toilet is pulled, sounds like the pen could be lodged in the drain pipe causeing the shower to drain slowly. The pen could be catching all sorts of things and will eventually cause a bigger clog.
You can remove the P-trap under your kitchen sink to reclaim your lost toys, it's fairly simple to remove the two nuts that hold it on. Here's a link that'll show you how
http://www.blackanddecker.com/Projec...781_10860.html
The lights you describe in your kitchen are florescent light fixtures and the plastic cover is just that, a plastic cover.