It should also go without saying that if you're using the farmhouse start, clean your stuff out of it first because if you don't you'll lose it all.
Clean your stuff out of any other start location containers you may be using, including any that are part of the vanilla game because they will NO LONGER BE SAFE STORAGE!!!
I highly recommend going with the order LOOT specifies.
Skyrim has a lot more flexibility in pursuit of the main quest, even when playing the default Helgen scenario.
Any mod that is more than pure mesh or texture replacements has the possibility to leave behind permanent changes to your save that you may not want. That said, should you insist on going forward with doing so you must adhere to the following: First things first.