Your question is a good one because it is somewhat rare. It should prove to coaches that we are all different and cannot train the same way. The first thing I must tell you is that what I have written for you is far from complete. I ran for 45 years and also coached. We are complex human beings and learn new things every day. I hope that you can find good counsel from a top coach, or running physical therapist or doctor.
In your case you have potential for speed development! First you will have to run lots of miles to build up your aerobic base. That part is not different for you than anyone else. Running on the balls of the feet is actually preferable to running on the heels or at mid foot. You do have different needs than all those people. You are also gifted!
For aerobic base building begin at the distance you are now able to run and do it easy and relaxed. If you cannot make it easy, then walk/jog it. It is very important that you learn relaxation techniques when you run. Do this by breathing slowly and deeply. Take care to blow out, more than you breathe in. (If you can breathe out of your nose, and not out of your mouth, that is the way to go. But the main thing is to relax and breathe deeply. We do not want fast breathing during a jog.) Relaxation is the key! Never ever worry about speed, this is where whole teams get into trouble.
One day per week, concentrate on speed building.
1. Do a 1 mile jog warmup; dynamic warmups like skipping, butt kicks, carioca, backward runs, and etc;
2. Then do 10 x 80, as follows: The first 80 would be at about 70% of your top speed, then run about 5% faster for each one after that. You might be running the last 2 x 80 at top speed.
3. Then warm down extremely well. Walk 1/2 mile, jog a mile, stretch.
*Add no more than 1 mile to your total mileage each week. (Some recommend adding 10%)
Be very careful not to over do it. If you have pain go see a running doctor. If it's not practical to see a running doctor, then find someone who knows runners. Perhaps you could email someone. The most important thing is to see someone about an injury as soon as possible. Tape and Motrin may solve your problem.
I do not recommend rigid orthotics...trust me I know from personal experience, and it is non-running doctors who prescribe them!
I know you as sorecalves123. I will check for your progress. May the fitness be with you!