I can relate to your problems, and tend to agree that the bike is too large for you. I am 5'7"" and ride a 51 cm frame, which fits perfectly. Another bike shop tried to sell me 56 cm frame.... my hands would never touch the handlebars. Also, I noted that you mention that you thrust your pelvis forward when running, you actually need to do the opposite thing in cycling and your core muscles might not like this at all and need some adapting and you therefore feel you are too far back. One thing you can do is align the front of your kneecap with the center of you pedal axle (drop a weight on a string from the kneecap to the floor and see where it hits your pedals, feet in 3-9 o'clock position). That gives you a good idea about butt-leg orientation on the bike. Certainly does nothing for a too long top tube.... good luck with finding the perfect bike.