Can I half-bake muffins now, and then complete bake them the rest of the way a couple days later when I want them "fresh"?

There's a big difference between what's possible with bread and with muffins or cakes because bread is from a dough and the rest is a batter. Bread dough has a lot of structure to begin because of the gluten, so you can partially cook it to set that structure and then crisp it up later.

You can't do the same with a batter as there's no structure. When you bake a batter the heat turns water to steam, and the leavening agents react, causing air to form. At the same time a crystalline structure forms around the sugar and starch, which traps the expanding gases and the structure expands upwards, i.e. rises because the shape of the pan restricts it to one direction. Once the expansion is complete cooking then completes the crystallization of the structure, making it semi-rigid. If you interrupt that process before it's complete the cake/muffin won't have the strength to hold up its expansion and the whole thing collapses into a dense, undercooked mess.

Fortunately for you muffins keep their freshness longer than bread, and also freeze well. Some fruit muffins actually get better with a couple of days in the refrigerator, you may want to try it with yours.

We make the muffin batter, pour it into liners, and freeze in the trays. Thaw overnight, then bake as usual.