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Most of the major diversions between your route and what we did recently involve going round hilly bits, which is fair enough. I'm glad we did Dartmoor and the Lake District, but I'd probably choose something a bit more direct for a 9-day trip.
One minor point of suggestion is a Plan B option approaching Fort Augustus; if the A82 is particularly busy, the path up the side of the canal from Bridge of Oich up to FA is flat, pretty smooth fast surface and very quiet w.r.t. other cycle/pedestrian traffic. Save something for the climb up General Wade's Military Road. Well worth the effort for the views at the top!
No reason really I don't think - I was thinking about that! I will probably amend that route, thanks :)