Quote Originally Posted by run it, ride it
I'm 5'5" with a short torso and the new bike is 54cm. Old bike is 52cm.

New bike is supposed to fit! What is wrong here?
Just a few thoughts that come to my mind....

I honestly don't see why a 2cm difference in frame size is going to suddenly mean the difference between total comfort and multiple excrutiating pains for you. I suspect something besides the 2cm frame size difference is at work here causing the pain issues.
Something to do with balance of weight, handlebars, handlebar position, leg/crank angle, seat position, whole body position.....etc. (and what was that "agressive angle" you say the bikeshop guy told you you had your handlebars set at?)
I am not sure that setting your seat all the way forward to get positioned "over" your long femurs is a good theory. Often we can get more whole body balance and power by having the seat BACK more, more behind the crank and pedals.

Anything the bike shop did you should give a few days to let your body try it. If your muscles have been used to a bad position for a while, then a new position will be pulling your body into a new conformation, which is bound to feel uncomfortable at first, and may cause muscles to object to the change for a while. People feel discomfort and pain differently as well. When we get a new saddle it can cause very real sitbone soreness for the first few days and then we feel very comfortable as our body adjusts. Commonly a new road bike feels "too high" to someone who has been used to a hybrid or mtn bike or comfort bike. After a week or two it doesn't seem too high at all. When I got my road bike I felt the handlebars were "too low and way too far away" and felt i was falling forward onto my hands. My hands hurt after riding. In reality I had not built up the torso strength needed to balance my body evenly over my seat, feet, and hands. After a month, it feels more comfortable and natural to me every day now, and my hands no longer hurt at all.

We should also remember that bike frame geometry and proportion varies, and certainly frames cannot be judged just by standover height. Not every 54cm frame is the same size. Rivendell frames for example have a different geometry, and so my 54cm Rivendell bike frame fits me perfectly at 5' 5'" height with an average woman's build. So no one here can tell me MY 54cm bike is "too big" for me at 5'5", because it's a totally perfect fit!
Just my 2 cents.