Some things to do on your trip:
1. When in La Paz, check out the witches' stands (brujerias) on many corners. They sell all sorts of potions and "magical" objects. My favorites were the overflowing bins of llama fetuses, which custom mandates be placed in the far left corner of every new home and building.
2. If you've got the time, I found Potosi in southern Bolivia far more exciting than Lake Titicaca. You can actually go inside the Cerro Rico and see miners "excavating" silver in 500 year-old mines by throwing sticks of TNT against the walls.
3. That said, you can overnight on the islands in the middle of the Lake for next to nothing, depending on your sense of adventure. Helps if you speak Spanish (or Aymara, or Quechua).
4. To avoid "soroche" (Peruvian word for altitude sickness) drink mate de coca or chew a big wad of coca leaves. That's what all the porters did while carrying stuff past me on the Inca trail.

Aguas Calientes is indeed eminently miss-able, but after four days on the Trail without a shower, the thermal baths were wonderful. If you take the train home from MP, splurge on the most expensive train ticket they offer. I went cattle class and was not pleased.

Have a wonderful trip.