Good news for you buddy, you are not the first person in the Navy to have a problem like this.
I had a decade long battle with shin splints until one the head athletic trainer in college got me fitted for custom made inserts. The pain was gone for good within a week. Custom inserts are the "one size fits all" solution to about 90% of all foot strike problems. I could have searched the world over and spent thousands of dollars on shoes without finding something that would work. I could take these inserts from my cleats to any other shoes, and my feet have been fine ever since.
The Navy has a program that will buy you a set of custom made inserts twice a year. If you are in OCS, it may not be the quick fix you need, but it could easily be a long term solution for you.
This is a program that everyone needs to know about. It's just a matter of time until you have a sailor on FEP because they can't pass the run. A lot of these guys can pass the run because running hurts like hell due to foot strike problems. Get these guys into medical and get them the tool they need to get fixed (or at least eliminate an excuse).