I would suggest if not in a great rush you might consider the following modifications to the Amaferanga route in order to avoid the A9, which is fast, but I wouldn't consider it enjoyable to cycle on for the most part. Although there are considerable variations in traffic level depending on time and location.
Via Crieff and Amulree is good!
1. I suggest taking the side road from Logierait to Pitlochry rather than going on to Ballinluig and up the A9 dual carriageway.
2. Suggest going through Dalwhinnie on the "old A9", taking a right after you pass the distillery and cross the railway then through Newtonmore and Kingussie thus avoiding the A9 again.
3. North of Aviemore again follow the "old A9" route to Carr Bridge, Tomatin and Moy, but instead of taking a right on the Craggie Brae to follow the NCN, carry on down to the junction with the A9 and follow it towards Inverness. (Short distance on busy road rather than tortuous route on quiet roads into Inverness)Take the first on the left after the summit off the A9 to follow a quieter road down to Inverness.
4 Immediately after crossing the Kessock Bridge take a left down a steep brae to sea level and follow the coast road through North Kessock towards Redcastle , Muir of Ord, Conon Bridge and Maryburgh and on to Dingwall. (less climbing, quiet route)
5 At Dingwall you have to choose to take the back road to Evanton, (quiet but hilly) or the coast road which is fairly quiet to the A9 junction at the bridge, then on to Foulis Ferry where you can turn left to access the back road again, but at a lower point (if that makes sense!) then on to the junction at Novar Toll for the Struie road over the hill to Bonar.
There is little scope for variation north of Bonar!
I would be surprised if you had problems with road surfaces on the routes i have suggested.