Hi, bigtex-1836,
Battle of the Alamo?
I think that your trip to Fort William depends on how much time you want to spend in the Trossachs. Many people who visit the Trossachs make the main part of their visit a boat ride on Loch Katrine aboard the Sir Walter Scott. If that's your plan, it's a two hour voyage. The Walt traverses the length of the loch, and if you want to hike back from Stronachlachar, it's about 12 miles on a relatively easy trail and paved road. You can also hire a bicycle for the return trip. If you're just looking for hiking, there are some really good hiking trails in the Trossachs. Most of them are fairly easy, and can be found on the WalkHighlands website.
From the Trossachs to Fort William is about a two hour drive via the A85/A84/A82. That will take you straight through Glencoe. Fort William is not that far from Glencoe, and there is a much greater choice of accommodation, so even if it means doubling back a little, you'd most likely be better off basing yourselves in Fort William for three days. You'd most likely end up seeing things that you'd missed on your first time through Glencoe.
The amount of nights you'll want to stay in Portree depends on how much you want to see. Based on previous experience, I'd say that three nights are adequate, four nights are even better. If you're planning to do a lot of hiking on Skye, there are many partial or full day hikes available. Again, the WalkHighlands website will give you a pretty good idea of what's available, although there are some good ones which aren't on the website. Raasay is good for a day by itself.
Once you leave Skye, you can spend the better part of your departure day heading up the west coast (God's Country - sorry, Texas!) on your way to Inverness. Once you cross the bridge, drive through Duirinish and Plockton, over the hill to Lochcarron, then follow the A896 to Kinlochewe, and on to Inverness from there. For a great side trip, you could take the Bealach-na-Ba pass to Applecross, then take the coast road around to Shieldaig. There are some good hikes in the Beinn Eighe/Glen Torridon area.
If you want to see the best of Loch Ness on your way south (If you decide to travel south along the loch), it's actually best seen from the eastern shore via the B862/B852, through Dores and Foyers. That will dump you out on to the A82 at Fort Augustus, which you can follow back south. However, you will be going back through Fort William and Glencoe, which you've already seen
For a slightly different return journey from Inverness, you could take the A96 to Nairn, the A939 to Ballater, and the A93 south through Glenshee and Blairgowrie, picking up the motorway to Edinburgh at Perth. That would give you a different perspective.
Whichever routes you decide to take, have a wonderful time in Scotland!
Best wishes and safe travels,
Mike (Auchterless)
p.s.: I'm assuming that you'll be taking the A830 from Fort William to Mallaig, and the ferry over to Armadale, then leaving Skye via the bridge. If that is your plan, please be sure to make a reservation for the ferry, and give yourselves enough time to visit some of the beautiful beaches along the way.