I'll be staying at Disney World for the second time (split stay between AKL and Pop Century). My first visit was at the end of August, so I'm betting that the weather will be much different, but I was wondering if anyone had any tips for a January trip?
I go in January and August every year. Yes, the weather will be much different in January. Generally, you won't have to deal with as much rain, although you should still bring an umbrella. You will want to check the weather before you pack and pack as if it could be 80 or it could be 40. I went about the same timeframe last January that you're going, and we got there, and it went from 70s to 80s to 40s and back up to 80s in the space of nine days. Mostly it should be in the 60s or so, but it's hard to tell.
Don't plan on riding Splash Mountain. It goes down every January. I wouldn't plan for waterparks either. But on the plus side, the castle will look like this:
As far as the crowds go, you won't see as heavy crowds as you see in August, but you will see some residual crowds from the holidays. The tour groups are the worst part of the crowds. With the marathon, just avoid Epcot on that Sunday and you'll be fine. I didn't notice a significant difference between the parks on the marathon weekend and the week other than normal weekend crowd fluctuations. That might be a good day for you to start out at AK and then go over to MK for EMH. I wouldn't expect AK to be crowded that day. It's actually more crowded on week days than the weekend, so a Saturday or Sunday is a good day for that park. The day before the marathon (Saturday) might be a good Epcot day.
As a general rule, avoid MK and DHS on weekends except if you are utilizing MK EMH on a weekend.
Also, am I allowed to add the Magical Express if I made a reservation already and didn't add it? I'll be heading back from Peru on Jan 5th, and since I'll be on a tour I won't know my flight info until late November. Will I still be able to add that info?
Yup. DVC owners book their trips up to 11 months out, so we always add our flight information later. They're used to this. You can add it right up until you go, but if you were to add your flight info just a few weeks ahead of time, they might not be able to get your luggage tags out to you in time, although you would still be able to use Magical Express. I don't see this being an issue in your case, though.