When is building upon the greater in prayer not considered permissible, given that the whispers ceased for an entire day and then doubt returned the following day? And should doubt then be treated like ordinary doubt, building upon the lesser, considering that the criterion for habitual doubt is its occurrence once every day?

The excessive doubt, which its owner is commanded to ignore, is the ingrained doubt (al-shakk al-mustankah). This is defined by Maliki فقهاء (jurists) as doubt that recurs, even once daily. If doubt accompanies you even once a day, then disregard it and pay no attention to it. However, if it comes to you one day and is absent the next, then build upon the lesser.