You mentioned all the possible things it could be: being a new rider, the saddle, the new aero position or your shorts. So, this is a process of elimination that many of us have been through... and it ain't cheap sometimes to figure it out.

It looks like you knew right away that the saddle that came with your bike was wrong for you and went to another that's not as bad. But you still have some pain. So, new rider pain could last a week or two. Beyond that, it's probably going to be the saddle or the shorts. Depending on where the pain is, I guess it could also be the fit ie: if you are stretched out too much and putting too much pressure on female parts.

Kind of delicate subject, but I hope you aren't wearing anything with seams that could rub/chafe your soft tissue, such as underwear. You may want to try putting chamois cream on the seams of your cycling shorts. Make sure you are washing your shorts between rides so you don't create a science project. All cycling shorts are not created equal and like saddles, the chamois that works perfect for one girl is not so good for another.

For me personally, I need a very minimal saddle (I use the Selle San Marco Aspide Glamour) and very minimal chamois (the Castelli Kiss Chamois is my favorite). Any more padding than this and I am in agony after about an hour. Although I am a little over-weight, I have virtually no rear end and I don't like my sit bones sinking down into padding.

Hope it works out to just be "new rider behind".