I thought you posed an excellent question, wanted to answer, but needed to sleep on it.
If you go by Jennifer's website strictly then I think scenario #1 makes the most sense. However, I do believe that information about the cell phones being shut off at 10:40 to be true (did not see this information on the website, but I trust the sleuthing and information that has been gathered after the fact).
So, just because the bed looked to be slept in, does not mean that it was Jennifer that slept in the bed. Remember Monday night would have been Jen's first night back at the condo from the cruise. Perhaps the brother slept in her bed and never made it. Likewise, just because the shower was wet and the towel was damp does not mean it was Jen that showered.
This is where it really gets creepy for me, because if that scene was staged, including the outfits laid out for work, this was someone who was obsessed with Jen. This was someone who had been in her apartment before. This was someone who had watched her closely and stalked her. Creepy, creepy, creepy! It reminds me of law student Lauren Giddings and her stalker/murderer Stephen McDaniel. Hannibal Lector and Silence of the Lambs creepy.
So, I believe the second scenario to be the correct scenario. The phone call ended at 9:57 with her BF and whatever happened to Jennifer happened just prior to the phones being powered off at 10:40 or immediately after they were powered off.
I appreciate everyone's theories regarding what happened to Jennifer. I wish we had more answers. I wish her family had her back home. It's so sad.