Will my stressful year be seen as a negative?
"Stressed out" could hurt you insofar as people who would give you otherwise positive recommendations might be tempted to tone them down. 

When asking for letters of recommendation, discuss these issues candidly with the prospective recommenders. Some might not care. Others might "care" but they might also be open to a discussion of extenuating circumstances. A few will have their opinions shaped by your behavior. If and when you identify such a person, you might want to withdraw your request for a recommendation from them.