Hi Katie -
Sorry about the hammer toe issue. And I am assuming you mean the toenail turned black, not the toe, right? You mentioned overpronation. Have you looked at other factors that might be leading to this, such as pelvic stability? Without seeing you run, I can only hazard a guess. The issue I have with most podiatrists is that (because this is how they are trained) is they only look at the foot and treat that. Often, the problem starts up higher, especially in populations where we sit a lot and lose connection with our core muscles and hip stabilizers. Not having adequate stability can cause issues (overpronation, etc) down the kinetic chain. If this is the case, correction at your feet alone can potentially open up other issues higher up.
Have you considered seeing a sports medicine doc? Is there an instructor in your area you can check in with and get video taped? A video will help you (and your instructor) see where your issues are - at more than just your feet.
As for the orthotics interfering with feeling the ground etc, yes they will. That’s a lot of correction, especially if you are already wearing Newtons.
Think about investigating a second opinion or finding an instructor to give you an assessment. Let us know how it goes.
Certified Chi Running and Chi Walking Instructor