I grind my own. I grind hard white winter berries for bread flour and soft white wheat berries to make pastry flour. Maybe you have a friend or neighbor with a grain mill or Vita-Mix. If not, I would try to find it in bulk at a HFS. My concern about the ww flour sitting in the grocery stores is that it stays on the shelf for a long time, losing nutrients.
I adapted a whole wheat recipe for bread, eliminating the white flour it called for. I don't use any extra yeast. As for muffins, I usually go 1/2 and 1/2, without any changes to the recipe. Same with pancakes.
For my muffin recipe, I think the muffins are better with some whole wheat. They are tastier. But when I went 100% they lost their texture and seemed to crumble apart. The pancakes also seem a bit more tender. My guess is that this is a gluten issue, or perhaps they are just heavier.