I agree with the bike fit. When I did mine, I was told how I needed to change my position, that I was putting too much weight on the handlebars (as you wisely noted of yourself), that I needed to put my butt further back on the saddle and flatten out my back, which felt like I was arching my back. It took some time and constant reminding myself from time to time to change something about my position, but for the most part I think I have it down now. I've been told I have good form, which was a great compliment.

The more weight you have on the handlebars, and the more tense you are, the more tense all your neck and shoulder muscles will be. On longer rides, you'll find you have neck pain. Your torso is supposed to support you for the most part, which was difficult for me at first because it hurt my crotch to sit the way I was supposed to, but that took time to get used to. As for the pain on the inside of your femur, you might find you need a different saddle, but get a proper fit first, work on your position and see if that fixes your problem.

By the way, when you are sitting properly, it opens up your chest and lungs and helps you get more air. This was a big help to me, as I tend to the be the one breathing way harder than anyone else!