I've ridden that line and can absolutely second that. Seeing the Highlands that way is a transcendent experience.

We B&B'd in Mallaig and took the ferry across to Skye the next morning -- glad to know it's still running. It all added up to one of my great trips of all time.

Probably the OP has already accomplished her trip by now! But i would just add to one of the posts above that renting a car in Ireland is more costly from an insurance standpoint than renting one in the UK, so there's another vote for flying to LHR, then GLA, then getting the train...