Top of Scotland 5-7 nights

Loganair flies from Kirkwall Airport (Orkneys) to Inverness.

I've taken that flight.

I've flown Loganair numerous times. They fly all over Scotland including the islands.

As for traveling between Cornwall and Scotland and stopping in between....there are trains. Lots of them.

You can fly to Paris from either Inverness or Aberdeen but neither is a nonstop.

It is possible to go from Inverness to Orkney by surface transport.

There is a bus at about 2.30pm from Inverness to Scrabster Ferry Port (Thurso) which connects with the evening Northlink ferry to Stromness. From Stromness there is a connecting bus to Kirkwall, but I really like Stromness as a place to stay and is a good base to explore mainland Orkney from.

Southbound you can board the ferry at about 9pm on a bed and breakfast basis while she is moored overnight at Stromness. Then have your included breakfast as the ship sails at 6.30am past the Old Man of Hoy to Scrabster, where the connecting bus picks you up for Inverness. That drops you at Inverness Bus and Rail Station. There are connecting buses and trains from there to Inverness Airport (the airport now has it's own railway station).
If you wanted to do surface travel between Cornwall and Inverness you could take a mid afternoon train from Cornwall to London Paddington then the Caledonian Sleeper from London Euston to Inverness, or the Riviera Sleeper Cornwall to London and the day train London Kings Cross to Inverness.

As far as I can see there are flights INV- AMS but not INV-Paris. ABZ is the same- AMS but not Paris flights.

You could fly to AMS then the Eurostar train (formerly Thalys) to Paris, rather than a connecting flight.

Three times a week there is the overnight ferry from Kirkwall to ABZ (leaves at 1145 pm, arrives at 7am). A connecting bus meets that ferry at ABZ ferry terminal to transfer you to the airport. All other airport bus journeys start from the close by bus station. A very civilised and well integrated journey.
Likewise 3 nights a week ABZ to Kirkwall at 5pm, arrives at 11pm.

The drive from INV to Thurso is part of the North Coast 500 trip. Hint John O'Groats is not the most northerly point. Like Lands End it is a bit of a let down IMHO. Yes go there if you want, but then make a stop at the true northerly mainland point of Duncansby Head. There will be no one there, not touristy like JoG.

On your drive between Wick and JoG (if you do it) visit Nybster Broch and the Whaligoe Steps.

So long as you tell the rental company your plans you should be able to rent a car at Inverness and take it over on either ferry to Orkney. If driving you could take the Pentland ferries route over to Orkney after visiting JoG.

Lots of options for you.

Based on your interest in the Orkney islands and John O'Groats then Skye would seem to be a bit of an outlier. 3 hours from Inverness to the Skye bridge, from where it's at least an hour to Portree (the main village) before you start exploring any sites or doing any walking (the main reason visitors come here). And 2 nights only gives you 1 full day to explore what is a very large island. From the Skye Bridge to John O'Groats would be an entire day of driving without stopping to see anything on the way there.

So it might be better to focus on Orkney - flying there from Inverness and renting a car to explore for say 3 nights, before flying back to Inverness with perhaps an additional 3 nights by car from Inverness to explore the north coast of the mainland.

I loved visiting Orkney last August and am going back in 2025. Stuart has given you excellent advice on the possibilities of onward flights. I flew in/out of Aberdeen via Amsterdam (from Seattle) and that worked well for me. I think I may plan that for 2025 so I can have the back up of the overnight ferry from Aberdeen to Kirkwall (although I am NOT a person who enjoys sea travel!). Taking Eurostar (formerly Thalys trains) to Paris from the station at Amsterdam seems like a good combination.

There are a lot of complaints online about service from Loganair and cancelled flights. I'd be sure you have some flex time in your schedule in case there is bad weather at Kirkwall which causes delays to the flight schedule. I, personally, had no delays in August on Aberdeen to Kirkwall, Kirkwall to Lerwick Shetland and Lerwick back to Kirkwall.

The Facebook page I was following was Flight Delays and Cancellations Orkney/Shetland Many posters seem to be locals and there is a lot of complaining or whinging I think is the UK term. Many are trying to get back and forth to Dr or hospital appointments in Aberdeen, Edinburgh or Glasgow but it's an interesting read.

Thanks everyone for all of the great advice. We have decided that Skye isn't going to work on this trip. We will fly in to Aberdeen and drive across and up the NC500 to the top then hopefully head over to the Orkneys before driving down via Inverness. The plan now is to then stop at Pitlorchy for a night and go to the Highland games there on the Saturday and fly out of Edinburgh on Sunday afternoon (direct flight to Paris with Easyjet - haven't flown with them for a few years but hopefully ok)

I have been e-mailed about a big bus tour this morning to Orkney (run by a Scottish company and aimed a domestic tourists so at a realistic price point).

One of the places they are visiting in Caithness is Mary Ann's Cottage at Dunnet- https://www.caithnessandsutherland.com/mary-anns-cottage/

I haven't heard of it, but it sounds an interesting diversion on your way round the NC500. It is also close to Castletown Beach (one of the glorious and unvisited beaches of the far north of Scotland) and to Dwarwick Pier- used by the Royal Family when visiting the Castle of Mey.

An interesting way to hear about such a place.

They are also stopping briefly at the better known (but not often mentioned on here) Old Keiss Castle

Hopefully the NC500 won't be too crowded in September or October. It has become very popular and I've read stories of people being stuck behind caravans of slow-moving camper vans. But I would imagine by the time you're there, it will be good.

6 nights, especially if you are wanting to include Orkney is the minimum. Don't try and pare it back!