Personally I'd take the train from Glasgow to Glenfinnan via Fort William, then go back to Fort William for one night.
The next day I'd take the bus from Fort William to Inverness and break my journey in Fort Augustus and at Urquhart Castle.
The direct route Glasgow to Inverness, then back to Edinburgh is the same track north of Perth, so you would run the same both ways.
The alternative as outlined in reply #1 would need the Citylink bus from Fort William to Inverness as no train for that leg, but the scenery to Fort William is worth the trip.
Peter's option is indeed the most scenic, by a very long way.
Don't stay a few days in Inverness if you want our best. This is a dull/largely modern city in the least Highland part of the Highlands and developed for the sort of tourist who doesn't actually want our "wild" landscapes.
That said, if you are reliant on public transport, you might be stuck with it as Inverness is the main transport hub for much of the north and you have a choice of tours that will take you to great places. Timberbush do one to Applecross and Torridon that is more of our very best. They also offer a 2 day tour to Skye that is worth it - all the 1 dayers by other firms let you down because the distance involved means you don't get enough time on the Island.
Or you could take the bus to Lochinver/Assynt and be right in amongst it!
Aviemore and Pitlochry are also good options with good choices for the Cairngorms.
Edited: 19 May 2024, 22:00I disagree with the assessment of Inverness in #5 . We used it as our base for touring that part of Scotland last year and had a lovely holiday. Good choice of accommodation and good choice of restaurants too. It made an ideal base for us and as it is a transport hub with small group tour companies such as Rabbies and Timberbush it may well be what you need.