Peru 2022!

In Cusco, the entire historic center, Mercado central de San Pedro, Plaza de Armas, the cathedral, piedra de 12 ángulos (12 angled stone), Iglesia de la Companía de Jesús, but most importantly Saqsaywaman.

In Lima, Convento de Santo Domingo, Palacio Del Gobierno, and Plaza de Armas. There is the Larcomar mall, and some beaches in the Miraflores area. For markets there is Miraflores Indian market/Inka Plaza.

We were on a National Geographic tour and would have enjoyed more time in both cities. We did enjoy Pisac, the Sacred Valley, and Ollantaytambo, but am not sure if you’d have time to visit them.

Shame you didn't build in enough time to do the Peru ho ho bus option for the country. A really handy and in expensive option. But for the 2.5 days at the end, you may want to look at whether you can fit in Pisco, or the Ballesta Islands by Peru Hop.
If you decide to stick in Lima, 2 must do's in my book is the Larco Museum - private collection of a lot of the country's pottery history including a separate building of all the erotic pottery.
Also, cheap but great place to watch locals have fun - Magic Water Circuit. Depending where you are, you could get there with the evening double decker bus tour. It stops there for a few hours. I believe it starts in Miraflores district. Otherwise, uber or taxi up. Entry is under $5. It is in the Guinness Book of World records as the largest fountain complex in the world (but that is 13 only), with interactive water play, laser light music shows and even this aging woman on her own enjoyed it.
Check what the G Adventure tour includes. If it doesn't include the Sacred Valley, then visit the Ollaytatambo inca complex, Moray site, and other Inca influence in the Sacred Valley. They are bound to include a visit to a chicheria (chicha is a rough fermented corn drink). It is pretty terrible, but if they have the 'frog game' (like bean bag toss with points on flipper blocks) the chicha will add to the hilarity.

Congratulations on booking the trip. You will love it.

I did a similar trip seven years ago and hiked the Inca Trail. Absolutely great trip. You don't have to be a world class athlete to hike the trail: some of areas of the trail are practically handicapped accessible. I trained by hiking several 5,000-7,000 foot peaks in NH on weekends, about a month prior to the hike. The Incas were master engineers. Getting up at 3:30 on the last day of the hike so you can see Machu Pichu as the sun rises is a memory that will last with me forever. The food that our guides prepared on the four days was outstanding. The scenery is spectacular. After four days, we took a train to Aguas Calientes and stayed one night and a hot shower before heading back to Cusco. The U.S. dollar did really well against the Peruvian currency, so it was fairly inexpensive.

We enjoyed Cusco, but three days there is certainly enough time. We hired a local cab driver named Elvis for very short money who took us to Sacsayhuaman, the Maras Salt mines (where we drank cold, delicious purple frosted drinks made from purple corn), the Moray Archeological site, and a small, native Andean village where we purchased hand made sweaters/scarves from the locals. All of these sights are worth a visit. (I think we paid him $50 American each -there were two of us-, pjus tip, and he was our tour guide for the entire day).

I had never seen such poverty as I saw on the outskirts of Cusco proper: people living in tin roofed huts, mud-based homes, etc.

The Peruvian food was pretty good, although it was laden with lots of potatoes, olive oil (perhaps corn), and a distinct, strong local spice, which may have been a Peruvian oregano. It was very strong and I didn't care too much for it. However, in downtown Cusco within walking distance of the Marriott Hotel (where we stayed) is a fantastic Italian restaurant where they bake their own, artisanal bread: I had one of the best dishes of bolognese pasta that I've ever had in my life. I was stunned at how good it was (and, I come from an Italian family).

Best of luck

As for Lima, we never left the airport so I have nothing to offer other than the bathroom I used had no toilets and no toilet seats: just a hole in the ground that I squatted over. Sorry.

Thanks for the tips! I scheduled 3 days prior and after just to cover my bases and make sure I see at least SOME of each place.

The Larco Museum looks really cool. I’m trying to make it a point to see the archeological museum of every place I go to see, like the Egyptian Museum in Cairo or the British Museum in London...so thanks for that tip :)

Are there llamas around the ruins in Cusco? My goal is to essentially find some time to see some ruins apart from the trail itself in Cusco, maybe some pretty streets and architecture? I also definitely want to eat some guinea pig and see some llamas :)

Thanks for the suggestions for Lima. I added that last second so I’m pretty clueless on the city, other than the fact that it’s supposed to be this food haven city in South America. No complaints, just sorta lacking the knowledge, and the time is limited anyways.

Get yourself a Lonely Planet book from the library or elsewhere, it will really help you plan and steer you well in Lima and elsewhere in Peru

I did a G Adventures tour of Ecuador/Peru in 2018. I didn't hike the Inca trail but there were some in my group that did. Your plan to acclimate is a good one. I didn't have much time in Cusco but I enjoyed the Inca Museum and watching a giant parade of children (it was some sort of private school festival). Drink lots of water on your first few days, it will help.

Lima is super spread out. I did two day tours with Haku Tours - a cooking class and a historic walking tour. The guide (same both days) picked me up at my hotel and provided all transport. The traffic is insane in Lima, leave yourself a lot of time to get to the airport, even if your flight leaves in the middle of the night (most back to the USA leave at midnight or later).

Peru is fabulous, we especially enjoyed Cusco, the sacred valley and Machu Picchu. We did a great tour there in 2019, 4 nights 5 days with PeruAgency that cost $799 pp. We did a full day in Cusco on arrival, the after returning from MP we had a day on our own. We saw all the key sites in the city and a couple of museums as well as four key archaeological Inca sites above the city.

Lima is interesting, but you need to take a tour. There are areas of the city that you don't want to go.

Be sure and take altitude sickness pills (need a prescription).

The dining in Peru is amazing. The potato came from there and there are hundreds of types of potatoes. We had meals where we were served several types of potatoes.

An alternative: basing in Pisac, then doing daytrips from there. It can work really well.
I hope that your trip is a great one!
I am done. The end.

One of my favorite trips ever! We tagged on an Amazon River cruise after Cusco. We went in 1994 and only had one day in Lima before we flew home at the end of our visit. Unfortunately my husband got the tourista and we were stuck in our hotel. I became ill on the flight home. Lucky me!
The flight from Lima to Cusco and back to Lima was horrifying and beautiful. Flying between snow covered, jagged peaks on each side of the plane was breathtakingly beautiful. The horrifying was getting served coffee with a lb of sugar in it. I immediately spit it out and gave it back to the flight attendant who immediately gave it to the man in front of me. I tried to stop him from drinking it to no avail. The flight made a stop and a young woman with a baby (no older than a few days) sat next to me. The baby was in an outfit with a slit in the bum and no diaper. Well, it went everywhere! When we landed, she ran off the plane. A man boarded and I refused to let him sit. It took a few minutes until the attendant finally understood my horrific Spanish. She put a blanket on the seat and the man sat in it.
Cusco was great. We were greeted and served coca tea in the lobby. It was tasty and was supposed to help with the altitude. I agree with the places the above posters mentioned to visit in Cusco. All were great.
Machu Picchu was wonderful. As we rode the bus down into the valley to catch the train back to Cusco, a very small boy helped us on the bus and then met us, with a wave and a smile, at each switchback all the way to the valley floor. We could see him running all the way. He missed one switchback though. He met us at the bus and helped us all off. Of course he got a tip from everyone. He was barefoot and he ran down a very steep mountain. Just amazed all of us.
Our train ride back to Cusco in the pitch black of night was a bit of a concern. We stopped numerous times so the crew could throw water on the brakes because they were burning. I’m sure they have better trains now.
I’m not sure what the toilet paper situation is these days, but in 94 you got two thin small squares, period.

You are going to have a great time. We surly did!