Could whole wheat flour be subbed for some portion of the all purpose? If so, how much would be reasonable? Thanks!

There's a lot of questions hiding inside this one question. For one: what kind of rye flour is specified? There are three kinds, basically - all ground to a different micron, making them less or more thirsty, aka in need of hydration/leavening. Most whole wheat flour is very thick, heavy, and thirsty. It looks like the proportion of rye:AP is something like 1:2.5

Whenever I'm substituting for the first time I start with 10 - 25% max. This way I can see, feel, and taste the change I've made immediately. Bread is very forgiving, actually, and if you're skilled enough to make pretzels, you'll see, along the way, what to do if the dough seems too thirsty or isn't rising as it's supposed to. I agree about the whole wheat pastry flour - it might be more like the rye you're using or substituting out.

Spelt flour is also often recommended as well.While Renee mentions luck w/ 100%, in this particular case, where Kim/recipe chef uses 1 cup rye flour and 2 1/2 cups AP flour (plus the fact that she is NOT including wh wheat flour- in spite of the fact that she created this recipe for her book called "Good to the Grain"- i would rec emailing and asking Kim. She may not look at the Hotline section (she is new to the 52 community)but you can click on her name which takes you to her member page- and then click on the envelope to send her a direct question. She should rcve that and respond.

(I just wonder if subing 100% wh wht for the AP would lessen the rye flavor or affect the pretzel texture or.... and i am just learning about all this.)

Try Bob's Red Mill Pastry or All purpose whole wheat flour. They have worked beautifully for me when substituting (completely) for white flour in recipes.