if anyone has any alternative suggestions
Seems a bit odd to deviate east to Boat of Garten, more miles for no apparent reason.
The NCN between Ardgay and Invershin was drawn up partly for the convenience of cyclists visiting a now closed Youth Hostel. Whilst the NCN route may be considered more scenic and carrying less traffic, it includes the need to carry your bike down a flight of stairs at the bridge crossing the river. I would suggest going via Bonar Bridge for a less tortuous and more level route with negligible difference in mileage, traffic volume will be minimal.
As already stated up thread, the JOG-Burwick ferry is seasonal, but the Gills Bay -St Margarets Hope service is year round.
It is further from Thurso to JOG than it is from Stromness to Kirkwall,difficult to understand why the much longer route is selected. The least energy sapping route for a cyclist between Thurso and Kirkwall would be via Scrabster, and not via Gills Bay or JO'G.
The route chosen between Alness and Ardgay is ok in summer, but you must keep abreast of the weather forecast before tackling it in October. There are no pubs, cafes or any places of respite going over the Struie Hill route. Following the lower NCN is a little longer in mileage but involves a lot less climbing and offers shops, pubs cafes etc in event of poor weather.
Much the same and worse could be expected on the section north from Lairg and along the north coast.