My biggest concern would be your visit to MP. I'm not sure how the Salkantay trek compares to the Inca trail, but most of the people we saw were pretty wiped post-trek. Huayna Picchu is a non-trivial hike on its own, so I worry that you might be too beat to enjoy your time there.
Also, what time do you plan on arriving and leaving MP? I would think a same-day return to Cuzco probably means a ~5 PM departure, so want to make sure you have enough time to enjoy MP without rushing through it.
As far as Lima, I would second the Larco Museum suggestion (and make sure not to miss the small erotic museum adjacent to the bigger building). There are lots of reasonably priced walking and bike tours through various districts that originate in Miraflores that are worth looking into. In particular, I would recommend a visit to Barranco (guided or otherwise).