I decided it was time to bottle the stout after 5 days of secondary. The beer was pretty clear prior to secondary anyway, and the gravity didn't change in the 5 days, so no big deal.
Step 1 of bottling is to delabel and sanitize all the beer bottles. Today we learned that washing out the bottles before adding them to the collection goes a long way to cleanliness. We had to throw out about 12 bottles because of gunk stuck on the bottom. Regardless, we still had enough bottles at the end to fill everything.