You should be able to substitute whole wheat for the whole red fife pretty well 1:1. You might have to adjust the hydration a bit depending on how much red fife was originally in the recipe. My experience with whole red fife is that it doesn’t absorb quite as much water as whole wheat, so you might need to go by feel a bit when mixing. You may need to add a bit more water if it feels really dry.
Agree with everything what Benny said. And it’s to your advantage that ordinary whole-wheat flour might need more water. Better that way around rather than whole wheat flour might needing less water.
I think you’ll do absolutely fine following the recipe with the flour you have in stock. If your dough is a bit dryer it won’t be the end of the world. If you don’t notice the difference then it will probably work just as well. If you think it feels a bit dry then slowly add in more water bit by bit till you’re happy.
Just did a quick calculation of the miche hydration. It comes in at 77% hydration. That plus the mix of flours looks like it’s in a good range for using ordinary whole wheat with a combination of spelt and rye. There is no exact correct hydration and there will be a range in which this recipe will work. Even if using the exact flour asked for in the recipe one still might need to make adjustments if need be. Not all spelt flours are the same and so too other grains. Depends on where they’re grown, where you live etc. Don’t think you should be that concerned. Enjoy the recipe.