I found running in Mjolnir Armor to be a tricky business. The entire suit is susceptible to jostling (unless you really strap it down XD) and it can feel a bit too clumsy to want to attempt anything athletic in.
That being said, there is still great merit in making functional shoes. After all, you don't want the covers slipping off or making clomping sounds.
You can follow Bevbor's example and make a
hinged shoe or you can omit the foot plate altogether and opt for the 2 piece boot cover (ankle and toe guard).
You may not be able to run the New York marathon but you can at least get around comfortably that way.