I think this is the source of the problem. The bike is probably too small which is why everything else isn't falling into place. You don't seem to have any abnormal dimensions. I just went round and round with issues about my girlfriend who races track. As with most women, she's got long legs and a short torso. Hense all of the "womens' specific" bikes out there. Unfortunately there aren't any womens' specific track frames. You look normal. The majority of bikes are designed for men with normal proportions.

Take that rule about 1" stand-over the TT with a grain of salt. And this especially doesn't apply to track bikes which have a higher bottom bracket which based on geometry, will bring the TT up, too. I've had great fitting bikes where my junk was sitting squarely on the TT. The TT of my current track racing bike (with which I've had a professional fitting by one of the best race fitters in Atlanta) sits squarely on my junk.

A lot of people can (and do) make smaller bikes work. You can set the seat back and extend the stem, but the place where you'll feel squirlly is when you lean forward to sprint. Because the stem and/or your chest is ahead of the front axle this is really weird and unbalanced. Not so weird if you don't know anything different. But, when you do try a bike that fits better you will feel ROCK SOLID on it with no exceptions.