Going in June, you'll have plenty of daylight. Around the solstice, it's daylight until about 11 p.m., and dawn arrives about 4 a.m.
I have a couple of suggestions, for what it's worth:
First, there's not a whole lot to do around Loch Lomond, but a cruise on the loch would help you get an appreciation for it. If the Maid of the Loch is back in operation by June, that would be the best way to see the loch. You could also hike up Ben Lomond, which is the easiest of the Munros to climb. You can then claim that you've "bagged" a Munro. There are great views of the loch from the summit.
If you're going to Skye from Fort William, you may want to consider taking the ferry from Mallaig to Armadale on the way there, and the A87 across the bridge on the way north. Unless you're planning to visit Eilean Donan Castle, in which case you definitely want to take the A87 from Invergarry.
If you're going from Portree to Wick on what appears to be day nine, you should try to get farther north than Ullapool. Lochinver, Scourie, Kinlochbervie, or Durness would be better bets, and not only would you have a good chance of finding accommodation, but you'd have less distance to Wick the next day. Achiltibuie and Achmelvich, although beautifully situated, don't offer much in the way of accommodation. Personally, I'd go with Scourie or Durness, if I had to stop midway to Wick, but Lochinver is a charming town, and Kinlochbervie has a couple of good small hotels (Kinlochbervie Hotel and the Old School).
Best wishes for your travels!
p.s.: If you're taking the Jacobite, make your reservation as soon as you finalize your plans. The train fills up very quickly during the summer months. There is only one train per day. You may want to consider taking the Jacobite to Mallaig, and the regular Scotrail train back to Fort William (or vice-versa). There are three choices of seating. If there are only two people in your party, you should consider the two-seater option in the first class open category.
If you take the Jacobite both ways, you'll have just under two hours on the ground in Mallaig, which should give you enough time to explore the village.