The current method of operating the Highland services dates from about 1995. Prior to that, the trains also carried Motorail wagons, and there were three services from London every night. I don't think the FW train worked into Edinburgh before 1995. The change came about because the Fort William service was going to be axed, so the Highland service would have just been an Inverness/Aberdeen train, splitting and joining at Edinburgh. A couple of sleepers for FW were hurriedly retained in the train, but took a much more roundabout route.
The Inverness and Fort William services both departed from Edinburgh along the E&G main line, but a few years ago the Fort William started using the Airdrie - Bathgate line instead. This allowed the trains to call at Queen Street Low Level, and the Westerton stop was axed. Previously, ScotRail ran a very early Queen Street - Westerton DMU to allow seated passengers to travel to FW on the Sleeper.
I think the change to running via Edinburgh was a few years earlier than that -- I remember going that way the first time I used the Fort William train in June 1991. My recollection is that the Fort William portion included Motorail vans and was quite long -- maybe 7 vehicles in total. I don't remember where the rest of the train was going, but I presume it was either Inverness or Aberdeen, but not both.
On that occasion the route was via the E&G all the way to Cowlairs, but at times the northbound train at least ran via Falkirk Grahamston, Cumbernauld and Springburn (I think I remember going this way in 2002).
My guess (but no more than that) is that the sleeper may have started going via Edinburgh when the Sprinters arrived in about 1988 and there was no longer an early loco-hauled departure from Queen Street for the London portion to be added to.
Back in the 1970s the Motorail trains were separate from the others and ran from Kensington Olympia, although I don't know if Fort William was served (we always went to/from Stirling or Perth); if it was, I presume the Motorail arrived there coupled to the Euston/King's Cross train.
There were also overnight services from Glasgow/ Edinburgh to Bristol; I think they joined the sections at Carstairs. I don’t think they went any further south than Bristol.
There was briefly a portion from Poole or somewhere, which must have joined the main train at Birmingham; I used it from Basingstoke to Glasgow in February 1990. It was only 3 coaches if I remember rightly. Splitting at Carstairs had stopped by then, and the whole train reversed in Glasgow to continue to Edinburgh.