Have to agree about the A82. At best it is less than pleasant, and in any of the months without an R in them, it's an intimidating nightmare composed of RVs, caravans, tourists driving along whilst looking anywhere but through the bloody windscreen, vans & trucks racing to achieve unrealistic delivery targets between Inverness, Fort William and Glasgow - you get the picture. At least you have an alternative, for the Inverness-Fort Augustus section, of taking the General Wade Road on the east side of Loch Ness, a delighfully scenic road that brings you within touching distance of the loch on a number of occasions. However, once at Fort Augustus there is once again no alternative to the A82. It's bearable as far as Invergarry, but then becomes utterly nasty again, particularly the drag strip along the stretch bordering Loch Lochy, which is where the world and his wife tailgates everyone else at 65-70 mph, and consequently has not a snowball's chance of seeing a cyclist ahead in sufficient time to prepare the correct overtaking procedure. Not only that, but this Easter it was Pothole Central, an utter disgrace. A little further on, you have the possibility of avoiding another section, by turning off at The Commando Memorial and taking the back road, following the Caledonian Canal, into Fort William.
If you should decide to use the eastern A9 cycle-route option, and end up in Edinburgh, I can recommend making a beeline to Peebles, from where there is a delightful road through Eskdale down to Langholm and Longtown. I'll leave you there, for someone else to pick up!