Hello again, Gandy79,
Just a few comments, since you asked:
As you're flying in to Edinburgh, don't hire your car until you are ready to head up north. Having a car in Edinburgh is a definite liability, unless your lodging provides free parking. If that's the case, then it may be worth hiring the car right away.
You may want to consider staying in Thurso instead of John O'Groats. That way, you can take the ferry out of Scrabster for your day trip to Orkney. There's absolutely nothing to do in John O'Groats, and it's not even the easternmost or northernmost part of the Scottish mainland. If there were sidewalks in John O'Groats, they'd be rolling them up well before 5:00 p.m. :)
It is a long drive from Thurso to Ullapool via the coast. There are no diagonal short cuts from the north coast to the west coast. Be sure to get an early start. You'll be stopping often to gaze at the awesome vistas.
When you take your day trip to the Lochinver area, be sure to take the B869 circular road via Stoer and Drumbeg. It's one of the most spectacular coastal roads in Scotland. However, if it's absolutely lashing down rain, take the unclassified "Wee Mad Road" south out of Lochinver for Achiltibuie. You can return to Ullapool via the Stac Pollaidh road.
You're going to have to backtrack if you want to visit Glenfinnan, as you're taking the Skye Bridge from Kyleakin to Kyle of Lochalsh. You'd be taking the A87 as far as Invergarry, then the A82 south to Fort William and Glencoe. Glenfinnan is about 20 miles west of Fort William on the A830. Unless you had your hearts set on visiting Eilean Donan castle, you'd be better off taking the ferry from Armadale to Mallaig, then taking the A830 on to Glenfinnan and Fort William, and visiting Glencoe from there. There is much to see along the 830.
I can recommend B&B and hotel accommodation on Harris and Skye, if you're still searching, plus a comfortable, but inexpensive B&B in Oban. Also Tobermory and Fionnphort on Mull.
Best wishes for your plans!
p.s.: Be sure to check with CalMac to find out if you'd be saving money on the Ullapool-Stornoway-Tarbert-Uig route by purchasing an island hopscotch ticket. And if you take the ferry from Armadale to Mallaig, you could add that voyage to your ticket.
p.p.s.: As you're definitely not going to St. Kilda, you may want to consider a day trip to the isolated peninsula of Knoydart. It's only accessible via a 16 mile hike in from Kinlochhourn, or by a boat from Mallaig. That's if you do end up in Mallaig. Inverie, the main (actually, only) village in Knoydart, is fascinating. You could have a pint at Britain's most isolated pub, hike off in one of several directions, or check out the house once owned by famous Nazi sympathizer Lord Brocket, who was made famous in the song "Seven Men of Knoydart."
You could even stay overnight on Knoydart. There are several very nice places to stay.