I've been to Lima a few times and actually like it a lot, it's not the most beautiful city in the world but in it's own way it has a lot of charm and there's plenty to occupy two days.

Pachacamac was a disappointment, I'm a big fan of ruins but compared to other sites I've been to this one was pretty boring. You can't get anywhere close to most of the structures so it's an hour or so of walking along a road in the desert and looking at some distant rocks... I'd move it pretty far down the list. (I did it independently, perhaps with a guide it would be more interesting).

Huaca Pucllana is a definite must see though, far more interesting, much easier to access. Pretty tasty restaurant at the site for a nice dinner.

Lima Centro has some impressive colonial buildings and I've spent several hours walking around. Convento de San Francisco is, imo, more interesting than the Catedral, although Pizarro's tomb in the Catedral is worth seeing as well. The areas around Lima Centro aren't the nicest so I'd suggest making that part of the trip during the day.

Museo de Oro is also a great pick, not just for the gold but for the arms museum in the same building as well. Several rooms packed full with weapons from all over the world.

Several smallish art museums worth going to as well, Museo de Art de Lima and the Museo de Arte Italiano are both on the southern end of Lima Centro. Pedro de Osma Museum in Barranco is worth an hour as well.

The food is amazing as well, the restaurant at Pucllana and Astrid y Gaston are amongst my favorites. Along with a fast-food-ish type place that sells anticuchos, I think it's called Pepe's or something close. The heart anticuchos are great for a cheap quick meal.

Enjoy! I haven't made it to the more popular destinations in South America yet in Argentina or Brazil so I can't compare but I've been to Peru several times in the last few years and have enjoyed everywhere I've been.