Bikerta,
Regarding midgies, plenty on Skye and the small isles ( eigg, muck, rum and canna), but virtually none on the western isles (bara, uists, benbecula, Harris and lewis), flies can be a problem at times though.
There is a bit more mileage going via the western isles, but certainly no more than 100 extra miles ( I think!). There's also the ferry from Oban to bara and the onward connection to eriskay to consider, that, although not many cycling miles, will take you a whole day - chance for a rest? (Sorry, I've written this the wrong way round for you)
I would never ever cycle the a82 on the north side of loch ness, a real twisty turny, tourist infested death trap. If you must take that route, follow the Dores road on the other side of the loch. The glens route to the east is great, but as you say, the hills are a bit more of a challenge.
My main concern is how I'm going to cope with the traffic in the deep south; Birmingham, and the Manchester - Liverpool gap don't fill me with joy! I'm doing the trip with my sister in law, and we're planning to take 3 weeks, cycling between 50 and 100 miles a day, staying on the wee roads, and camping whenever possible. If you wanted the option to meet up en route, we could swap contact details nearer the time. It would be great to share stories over a glass of lemonade!
Regards,
Ali