You're right about not having enough time to see everything! I've been to Scotland 25 times, and I'm not even close to seeing all that I want to see!
You may have to skip Glen Etive if you want to make that 13:40 ferry out of Mallaig. Glen Etive is longer than it appears on the map, and because the road through the glen is single track with passing places, you're not going to make much more than 15 to 20 m.p.h.
The roads from Oban to Mallaig are good - well developed two lane roads. If you're going by way of Glencoe, you'll probably want to stop to walk for a bit, and/or take photographs. Make sure to give yourselves enough time to get to Mallaig. Fort William to Mallaig via the A830 is less than 50 miles, but you'll need about 90 minutes for the journey. Don't forget that you need to get to the ferry terminal at least 30 minutes before departure time.
The ferry trip is only 35 minutes, and they don't serve full meals on short haul ferries, so you may be able to get tea/coffee/soft drinks, and packets of crisps. Best thing to do is to get some takeaway sandwiches from the Co-op in Mallaig once you get there. (If you have time) The Co-op is about a three or four minute walk from the ferry terminal. As there are three of you traveling, one could stay with the car in the ferry line while the others go to get food. There is a small takeaway in Armadale, once you get to Skye. After that, your next place to eat would be in Broadford.
If you've made reservations for the 13:40 ferry, try your best to get there in time. As the projected tidal tables have cancelled all the following scheduled sailings until 18:00, that last ferry is going to be fully booked. If, once you get to Fort William, you think you're not going to make it, then take the A82 up to Invergarry and the A87 to Skye. If that happens, call CalMac to see if you can get a refund. Chances are the 13:40 will be fully booked, so if you let them know ahead of time, CalMac can give someone else your space.
As far as your choice of the northern or southern route from Portree to Inverness, either route passes through spectacular scenery. However, if you're planning on visiting Urquhart Castle, you should take the A87 to Loch Cluanie, the A887 to Invermoriston, and the A82 north to Inverness. My personal preference would be via the A890, as it features spectacular views over Loch Carron. You could still visit Urquhart Castle from Inverness. It's a fairly short drive down the west bank of Loch Ness.
The good thing about when you're traveling is that there will be lots of daylight hours. As you get closer to the summer equinox, you'll have broad daylight until well past 10 p.m.
Best wishes for your travels. Enjoy Scotland!
If I may say so, you'll definitely be back!