Here's my tuppence, for what it's worth:
Day 1: Arrive Edinburgh/Glasgow, spend part of the day exploring on foot and by public transportation. Spend the night in Edinburgh.
Day 2.: Continue to explore Edinburgh. Spend the night.
Day 3: Pick up a car at EDI. Drive to Aberdeen. There is a heck of a lot to see and do in the Aberdeen area. There are several excellent castles to explore, including Dunnottar, Crathes, Craigievar, Fyvie, Drum, and Haddo House. There is a lot of hiking/walking to be done as well, within and without the city. Spend the night.
Day 4: Drive to Inverness. Ideally, you should drive up to the Moray coast, and explore some of the fishing villages. Enjoy some Cullen Skink in Cullen. Overnight in Inverness.
Day 5: Pick out a scenic route to Ullapool from Inverness. There are many. Overnight in Ullapool.
Day 6: Morning CalMac ferry to Stornoway. Arrive Stornoway at 1:00 p.m. Drive to Callanish Standing Stones and Dun Carloway broch. Spend the night in or around Stornoway.
Day 7: Head south to Harris, and visit some of the stunning beaches there. Take the Golden Road. Walk out to the 14th. century church from the village of Northton. Spend the night in or around Tarbert.
Day 8: Continue to Explore Harris. Overnight there.
Day 9: Ferry from Tarbert to Uig, on Skye. Be careful here, as the ferries leave at a different time each day. Overnight on Skye,
Day 10: Explore Skye. Overnight somewhere central
Day 11: Continue to Explore Skye. Take a boat trip from Elgol Overnight at same lodging.
Day 12: Ferry from Armadale on Skye to Mallaig. Drive to Aviemore. Overnight in Aviemore.
Day 13: Explore Aviemore area and Cairngorm National Park. Overnight in Aviemore, or drive south toward Edinburgh.
Day 14: Return to Edinburgh or Glasgow, and overnight there. Or return to Edinburgh/Glasgow on day 13 and return the car at EDI/GLA on the morning of day 14.
You'll notice that I've left out Orkney altogether. Unless you're interested in Neolithic sites, you really wouldn't have enough time to get to Orkney and fit in the Outer Hebrides. Kirkwall to Ullapool is pretty much a full day's drive. The scenery is astonishing, but you wouldn't have time to stop and enjoy it. I understand that you want to see as much as you possibly can in your two weeks, but you need to get out of the car to really get a feel for the Scottish countryside. There is lots of good hiking and countryside walking on all of these routes and destinations.
Most of the routes I've suggested are fairly short drives of three to four hours. The only long drives would be Aberdeen to Inverness via the Moray coast, but you can easily shorten it, or skip driving down in to every village. Aberdeen to Inverness by the direct route is only three hours. The other long drive would be from Skye to Aviemore.
There is really no "best" time of year to visit Scotland. I've been there in every month except October. You'll get the most daylight hours in June, and the best weather any time between May and September. There is more competition for accommodation from mid-June to the end of August. Be sure when you've solidified your plans to make the ferry reservations. You can do that on the internet, or by telephone. You can save some money by getting an Island Hopscotch ticket, for your route from Ullapool to Stornoway, Tarbert to Uig, and Armadale to Mallaig.
I hope that gets you started. It's a beautiful country!
p.s.: Just looked at your day 12 RS route from Inverness to St. Andrews by way of Pitlochry and Ballater. You'd have to be a real masochist to attempt that drive in one day!