Nowadays there is another midge repellent - Smidge - which has been developed by Scottish scientists. It's worked for me. https://www.smidgeup.com/
Given the choice I'd avoid June, July and August though. I walked the Great Glen Way from Fort William to Inverness in May two years ago and really enjoyed it. It's a good way to see the canal without hiring a boat.
Despite what Nick says, I found Inverness very interesting. Banavie locks, Fort Augustus and Urquhart Castle are also worth visiting.
Accommodation along the Glen is sparse, but we stayed at nice B&B's in Spean Bridge, Fort Augustus, Drumnadrochit and Lochend.