One thing working in your favor is that January is NOT "high season". It IS, however considered rainy season. We were in Aguas Caliente three days ago and it would sprinke/light rain around 5pm.
A couple of thoughts: Perurail runs from Cusco to MP between 6-8 AM and it is full of people signed up for day trips. Those people then go up the hill and it gets crowded at the ruins. Around 11 am, there were lots of people coming to the ruins. We saw groups from Japan and Germany crowding up with their guides touring them in their language. This created bottlenecks. Also, because of the challanges of the steps, one will find themselves going nowhere fast in the crowd. As a result, our #1 objective was to be there early!! I cannot emphasise that enough. It is also nice to be able to get pictures of the ruins a minimal number of people in them.
What we did was to land in LIM and fly LAN to CUZ on the 7:45 am flight. We were booked on the 9:05 as "insurance" for customs delays. As we zipped through, LAN let us go on the earlier flight at no charge. Nonetheless, after landing in CUZ, we hired a cab to take us to our hotel to drop off our bags. Note Perurails
terms regarding luggage. Besides, you WILL NOT want to carry luggage far in Aguas. Sidewalks are steep with lots of steps.
With only laptop type backpacks with clothes, camera, etc., the cab drove us to Ollanta. The drive was a bit over an hour and a half. We paid a premium price ($60) for our family of four to be in one of those 9 passengar vans. When buying tickets on Perurail, Ollanta is referred to as "Sacred Valley".
In Ollanta, we were a bit early so we snacked on some local "fast food" outside the station gate before boarding the 12:58pm train. Its one of the less expensive trains at $37. Perurail says they want you there 30 minutes before departure as they will check your ticket against your passport.
Upon arriving in Aguas Calliente, we checked into a B&B, bought the necessary bus tickets ($17) for the next day, spent a little time in the market, ate and called it a day. In the morning, we checked out (B&B held our backpacks) and headed for the bus. Although the buses start their runs around 5:30am, we "slept in" and got on a bus around 7:30. At that time, the line was long enough that we had to wait and watch a full bus depart and get on another.
By noon, the crowds made us miserable, so we headed down the hill as rain clouds stared moving in. I can't imagine how crowded it gets in high season. We got our backpacks and took the 1:37 back to Ollanta and picked up a more reasonable priced $35 cab back to Cusco, arriving just short of 5 pm.
Should you desire, one can get two 1-way tickets Ollanta->MP and MP->Cusco. Again the MP->Cusco trains will be full of the day trippers and those trains only run from around 4p to 7:30p. As a result, I would suggest you look at your train time/station options and fill in the blanks from there.
Don't forget to get your tickets to the ruins early. Though I doubt the visitor limit will be an issue in January, its better to do it from the comfort of ones home. One cannot buy tickets to the ruins at the gate. We followed these
instructions to get the tickets a couple months early and things went well. The LAN flight from Cusco to LIM was packed on an Airbus 319.
Hope you have as much fun on your trip as we had. In fact, we are still in Lima for a couple more days.