If you're going during school holidays, it would be wise to pre-book accommodation as it does get incredibly busy. Make sure you get off the main route sometimes - you don't have to go far to have whole beaches to yourself, even in busy periods (some people seem to take pride in doing the route in 2 days, have no idea why and they miss so much).
The Black Isle and Nigg Ferry, Dornoch (there are seals along the coast here), the glens to the west of Brora and Helmsdale 9excellent fish and chips in Helmsdale) which are usually incredibly quiet and very lovely.
You could visit Croick Church and see the messages scratched in the windows by the families moved from their homes during the clearances - very atmospheric.
Best thing about John O' Groats (apart from the road out!) is the signpost and the foot ferry to Orkney - as said above, if you can get to Orkney it is worth the trip (if the weather is fine). St Magnus' Cathedral at Kirkwall is amazing, Skara Brae and Ring of Brodgar well worth a visit and we really like Stromness.
All of the west coast is beautiful, the Bealach na Ba is a wonderful drive but you need to be aware that some visitors drive it when they probably shouldn't and it makes for quite a bit of reversing and pulling over.
Skye - make sure you've got your accommodation booked before you go and visit the Oyster Shed at Carbost if you like seafood - far less pretentious and for less expensive than a lot of seafood spots on the west coast.
Inverewe Garden is beautiful.
There are so many fantastic beaches on the West Coast - all you need is the weather!