The ball of your foot should be directly over the pedal spindle for road racing. Track riders sometimes move their feet back more. It sounds like you are on the right track now.
In earlier posts, you said you had pain 1.5 hours into a ride. Your latest post says you are getting pain at 1 hour of riding. This is a trend in the wrong direction. It could be nothing, but it could be a sign that what you are doing to get well is not working.
Just an observation, but I am a little suspicious of your physical therapy. You say you are using ankle weights. Ankle weights typically weigh around 2-5 lbs. Unless you are doing 10,000 repetitions of an exercise, this is hardly enough resistance for even an elderly person with poor leg strength.
The best exercise for islolating the quadriceps and knee joint are leg extensions done on a machine, which doesn't sound like what you are doing. I'm curious about your P.T. alltogether, because stress fractures normally require no treatment (casts) other than the passage of time. Since your leg probably wasn't in a cast you could still move it and maintain the majority of your muscle mass.
The isolation from movement in a cast is what accelerates muscle atrophy. Even walking to the bathroom is enough stimulus to maintain "normal" muscle mass. Obviously, strength and size from hard training won't be as well maintained, but for the most part you shouldn't suffer from too much atrophy, which makes me wonder why you are using light ankle weights or in therapy at all.
I can only speak for myself, but if it were me I would have never gone to P.T. or a doctor in the first place, other than to have a x-ray to confirm what was wrong. I would focus on riding my trainer until I felt confident enough to get back on the road.
Stress fractures can be worse than a clean break, and can take longer to heal as well. Short of the passage of time, there is really nothing that anyone can do for you. If your insurance pays for everything great, but if you are paying out of pocket, that money would be much better spent on new pedals/wheels/etc.
I've had stress fractures before and I know how painful they can be. I think you would have been able to ride a trainer with light resistance without any problems from day one on the fracture. 30-60 minutes a day would have eliminated the need for physical therapy (if it even helped at all), and it would greatly accelerate the healing process by increasing the flow of nutrient-rich blood to the bones with far greater effect than standard P.T. exercises. Most importantly, you would be riding, and riding is sport-specific to riding. Ankle weights are specific to lifting ankle weights.
Some people might think I'm way off base, but why go back to your doctor or therapy unless there is actually something they can do to heal you? When you go back, will you doctor actually heal your leg or just talk to you? Do you know of any other profession where you pay $100 or more for nothing in return except 10 minutes of conversation? That's very often what a follow-up (or initial) visit to a doctor is.
Nature endowed mammals with a rich nervous system that registers pain when something is wrong. Let pain be your guide. You will know when your leg has healed because it won't hurt any more. Why pay someone a lot of money to tell you what you already know?
If I had some AK-47 rounds in my chest, I would see a doctor. But for something like this, I wouldn't waste my time or money.
The ILT will give you a boat load of leg strength. If you serious about riding, I feel you would be much better served by doing this. Additionally, how did you get the stress fractures? If you love riding, consider stopping the activity (running?) that caused them in the first place.
Just my observations, Andrew, don't take it the wrong way. I'm not trying to say your doctor or therapy is bad, I just don't think they can do much for you with this particular injury.
Do whatever makes you happy!!!
Good Luck!!!