Hi Amrita, I would go ahead and add the sugar or honey in with the flour and water during the autolyse. This is more of a modified version of an autolyse, so I think it would be fine to add the yeast in as well, and just incorporate the salt after the autolyse. Providing a 20-30 minute pause before adding the salt and kneading your dough will definitely make a difference when making 100% whole wheat bread. This will allow time for the bran to soften so that it doesn't cut into the gluten as much, which will lead to a more productive kneading process and a better rise. 

Barb

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