I am deciding on flights for a trip in November. I'll be wrapping up a 4 day trek on the Inca Trail on November 22nd. I am trying to decide on which Cusco-Lima flight to catch on November 23rd in order to catch an 11:30 p.m. int'l departure out of Lima. My preference is to take a flight late in the day on the 23rd (something around a 6 p.m. departure) so that I can have another day to explore Cusco. But I've read alot regarding reliability of Cusco-Lima flights and wonder if I should instead take an early flight (something around 10 a.m.) instead and try to do a guided tour of Lima during my layover. I'd rather have the time in Cusco and save Lima for another time, but would appreciate advice!

I'm not an expert on this but did some research before we made a similar decision for May trip to Perú; Cusco is a fair weather airport and is really prone to delays. We decided that a 5-6 hour layover in Lima would account for delays but not cancellations and decided that was enough for us. However, that was May when weather patterns tend to be dry with limited wind. You are going in November which has a whole different weather profile. You can look at averages here:
https://weatherspark.com/averages/33654/Cusco-Peru

When will you be back in Cusco? I hope you are not trying to get all the way from Aguas Calientes to Lima on the day of your international flight.

I would take the earliest possible flight that you can reasonably make, due to the chance of delays and even cancellations. If even one flight is cancelled, it can overfill all of the other flights. Although November wouldn't normally be high season, you are around the US holidays so I'm not sure you would be put on the next flight (only the 'next available').

If you have the option, buy your flights with the connection to Cusco included in the same ticket.

As everyone else says, take the earlier flight. Give yourself enough cushion for your connection. The airport is situated such that it requires an odd approach and takeoff path and the wind can play havoc with them. That becomes a bigger problem later in the day. Cusco is the only airport I’ve ever been in where they post signs warning you about the possibility of weather delays. Obviously, weather can hamper flight schedules anywhere in the world. At that airport, they feel they have to specifically tell you.

We were in a similar situation and took the morning flight (which landed right on time, but as others have posted, you never know). We took a short guided tour in Lima through Aracari Tours. Obviously you can't see much in a few hours, but the guide will know the best way to get around. We also had a driver so did not have to worry about parking at sights - he would drop us off and then just disappear somewhere, and the guide would summon him back. It was efficient without feeling rushed. (I am not sure we would have booked the guided tour just in Lima, but it was part of a 10-day trip in the Sacred Valley, and they threw in Lima at the end.It was well worth it.)

Thanks everyone! I will be taking the train back from Aguas Calientas the day before, so it's not the same day as flying out. After everyone's input, seems like the best bet is one of the first flights out of Cusco in the morning and do a day of guided touring in Lima before catching my flight back to the U.S.