What you said, pretty much sums it up.
If MK is still open, take the internal shuttle back to the Settlement, boat to MK, and bus to Pop.
If MK has closed, take the internal shuttle to the Outpost. If Epcot or Studios is still open, take the bus to there, and then bus to Pop. If everything has closed, take the bus to DTD and transfer there. Remember to take EMH into account; for transportation purposes, a park is still "open" until the end of EMH.
You can take a taxi, but you still need to first take the shuttle to the Outpost. I don't recall seeing many taxis hanging out around FtW, so you might need to call one (407-422-2222), or ask the front desk to call one for you.
The internal shuttle runs well into the early morning hours; no worries there.