There's no bus from the Fort to MK, except when the boats are not operating, usually due to weather.From FW catch the MK bus and then transfer to the Pop bus no security screening is required.
can not say for sure but from pics I have seen you will have to go thru security both waysTraveling from Pop Century to Fort Wilderness catching the boat at Magic Kingdom. with the security stations moved will we need to past through security getting off the bus and onto the boat? How about the return trip?