One day independent trip to Machu Picchu
Kolibri Expeditions provides plane tickets from Lima, train to Machu Picchu and private transport between Cusco and Ollantaytambo. You are collected at the airport and you will be driven to Ollantaytambo for the 10.45 train to Machu Picchu. If time permits, you may do a quick visit to the Cusco Main Square (Plaza de Armas) and Sacsayhuaman. In some cases with very early flights from Lima it may be possible to check out the garden of the Pakaritampu hotel for Bearded Mountaineer.
The earliest flights from Lima usually arrive around 7am. The transport to Ollantaytambo takes 1h45min.
Two day independent day trip to Machu Picchu
The two day program gives you a little more time. At arrival in Cusco, you go to Plaza de Armas with the Cathedral and the fortress of Sacsayhuaman (entrance fees not included). The driver will take you to Ollantaytambo, with a stop at Laguna Huaypo on the way for wetland birds such as Puna and Andean Teal, Andean Duck, Andean Gull, Andean Coot, Puna Ibis, Many-colored Rush-Tyrant, Wren-like Rush-bird, Yellow-winged Blackbird and many more. When you arrive to Ollantaytambo you may want to visit the spectacular Archaeological site (entrance fee not included) or photograph birds in th gardens of hotel Pakaritampu. One may find Bearded Mountaineer and Black-tailed Trainbearer
Later you return to Cusco to see some of the town such as Plaza de Armas with the Cathedral and the fortress of Sacsayhuaman (entrance fees not in the afternoon you take the train to Machu Picchu for an overnight stay.
The next day you have a full day at Machu Picchu and Aguas Calientes to explore the ruins and birdwatching. There is a good field guide for Machu Picchu which will help you ID the birds you see. In the afternoon you return to Ollantaytambo or Cusco.
Note the option of staying at the very fancy Inkaterra Machu Picchu Pueblo Hotel, which has hummingbird feeders, fruitfeeders for tanagers and often Andean Cock-of-the-Rock in the garden. It is a bit costly, but this is compensated by the great birding and bird photography possibilities, the advantage of guides to consult, a fantastic three course gourmet dinner and an abundant breakfast. Note that access to the gardens at Machu Picchu Pueblo Hotel is only for the guests staying there.