Some good advice already, I'd agree with most of what B cereus has said, I don't have much to add which isn't more of the same. I've done most of the NC500 roads, but before it was so well publicised. It includes some of the best of Scotland, but other sections could be missed or improved upon. For large sections, there are no alternative routes, if it's busy, you're stuck with it. The Eastern section, from John O Groats to Inverness I'd skip, take B cereus's advice to retrace to Bettyhill and south via Lairg, or jump on the train. I've ridden worse than that section, just IMO it's two or three days that could be better spent elsewhere.
I love touring in Scotland, just the feeling of space and how quickly the scenery changes. I usually go May or September, it's a gamble on the weather but there's been more glorious than terrible and I've been quite lucky at avoiding midges. In eight tours, about 20 weeks, I've only had one where the weather was foul for more than three consecutive days.
You're not going to see it all, so there's a choice to be made whether to cover a lot of Scotland or see more of a smaller area. I think the Hebridean Way is around 200 miles, but IMO a better tour of the Hebrides would be twice that. If you're going to cover more of Scotland, I'd include a trip out to Ardnamurchan, the most Westerly point on the British Mainland, you can drop on to Mull with a short ferry from there and a short ride and another short ferry back to Oban.
I hope you've not been put off the train, there's some great Scottish journeys, irrespective of conductors and lettuce. There's a bonkers line from Glasgow to Fort William, that only exists so the gentry could go hunting, over Rannoch Moor and Glencoe, familiar to those who've watched James Bond Skyfall, then on to Mallaig on the Jacobean line which might be familiar to Harry Potter fans. I think all, or most, Scotrail journeys require a bike reservation, but I've always found them easy to obtain. I have no qualms about mixing the train/bus and cycling if I'm touring, rather than a challenge ride.
Whatever you do, you'll have a great tour, for myself, starting in Inverness, I'd follow the Loch to Fort William and stay West of there till heading home.