Which park is best to start off with?
I say Universal, if you're parking in the parking garage and come out, the closest park is Universal, so I would just head straight towards that park, especially since most of the time Universal does early entry. But it is only limited to certain people (certain on-site hotel guests, vacation packages, ect), however, if you do not have those things, you can still go inside the park and while you're stopped at a certain point, you can at least enjoy the main Universal gift shop at the beginning of the park and they do typically let guests in (even those who do not have early entry) 15 minutes (and on rare occasions more) early.
What rides are a must?
Depends on what your desires are. If you're Potter fans head over to the Diagon Alley straight away (or Hogsmeade if you decide to not go to Universal, but Islands of Adventure instead). Or download the Universal app prior to going to the parks and watch the wait times before you go on your trip, to see which wait times are the highest, that way you know which rides are the most popular and go on those rides before the wait becomes much higher as it typically does as they day progresses. Another idea is to simply do the research online and read the descriptions of the rides to see which ones you and your family members want to enjoy as
@damo said.
Also, lastly, I suggest that if you want to go on a ride which requires to store all your belongings (yes, bags and including your phone, wallet, change, and anything else in your pockets) which are: Rip Ride Rocket, The Hulk, The Dragon Challenge, that you might go on those rides first depending which park you're at first, as even with low wait times the struggle to get a locker can be stressful and claustrophobic depending where you are. But that's only if you want to go on those rides, which if you have teen children I have a feeling they might want to go on them unless they don't like coasters.
Where does Hogwarts Express take you too? and do you pay for this train ride?
As others have stated, in a way, yes, as you need to have park-to-park admission in order to go on the Hogwarts Express since it isn't just a ride, but transportation to one park to another. Which you're planning to do anyway, so no additional cost to you! They even have people waiting outside of Kings Cross to remind you to have your ticket out.
How do I get from IOA to Universal or vice versa?
Either walk, or ride the Hogwarts Express is the simple answer. There is boat transportation in the City Walk, but not directly from one park to another. So, it's either the express, or walking. And quite honestly, if you really want to experience the Hogwarts Express as a
ride, that's great, but if you're focusing on just the transportation aspect and the wait is rather long, just walk. In the time you're waiting, you could be walking. The walk from one park to another isn't bad.