Hi, it sounds like a wonderful itinerary! I agree that 3 nights might be a bit much for Elgin, but it depends on what you intend to see/do there. The cathedral ruins are wonderful, though, and you can certainly do some drives to nearby coastal towns while you're there. If you are continuing your drive down the coastline to Edinburgh, you can't go wrong stopping at the Bullers of Buchan and the Slains Castle ruins (aka New Slains Castle) near Cruden Bay. They are both magnificent and are easy to get to as they are right off the main coastal road.
With regards to Loch Ness, I agree with the others that you could easily leave that off without missing much.
Mull is an incredible island and I'm very glad you're going there. Tobermory is charming and there is a lot you can see and do there. I stayed 4 nights in one of the harbor B&Bs and parked in one of the free car lots on the harbor. It's lovely to be able to walk down through the shops and restaurants that line the harbor. Bring your camera as it's very photogenic. You can visit the Isle of Mull Cheese Shop (Sgriob-ruadh Farm), which is about a mile from the harbor. There are self-guided tours to meet the farm animals and learn about traditional cheese making. There is also a cafe and a farm shop.
Also, there is a short walk from the harbor car park along the wooded hillside to Aros Park with woodland trails, a lochan and really nice waterfalls. A walk from the other end of Main Street leads along a coastal path to the Rubha Nan Gall Lighthouse. There are amazing views out over the Sound of Mull. And another short walk up the hill towards Baliscate leads to the Baliscate Standing Stones. Nearby is the site of the Baliscate Chapel, the subject of a BBC archaeology dig.
You also might want to stop at Isle of Mull Pottery, which is just beautiful. They sell some in the shops along the harbor but the main shop is in the town up above Main St. (you will pass it if you go to Calgary).
The Tobermory Bakery is wonderful—definitely stop here for one of their delectable pastries, take-away sandwiches and coffee or tea. Their Millionaire's Shortbread is incredible! There is a shop at the end of the harbor that is farthest from the ferry terminal that sells handmade chocolate with a tea room, and along the way are some very nice gift shops - I bought half my souvenirs in Mull (and I'm picky about stuff like that). Lots of nice restaurants, too. There is also a catch-and-release aquarium that is interesting, too.
I agree with Allan about Calgary Beach, which is about a 30-40 minute drive from Tobermory. It's very narrow and the single track roads run through the mountains with some switchbacks, so you will need to go slow through much of it. It's well worth a visit to see the beautiful beach, though. On your way back, you could stop at Glengorm Castle. This is a private castle so you can only see the outside (in a gorgeous setting along the water), but they have a nice cafe there where you can stop have tea and cakes in a very lovely setting. I stopped there for tea, then walked around the gardens and then down to the sea. It was a perfect afternoon.
I also agree with Allan about scheduling a buffer day for the tour. My tour was cancelled and unfortunately, I couldn't fit in another day. I would probably not invest too much time in one, so would go with the 3 hour tour that includes Iona. Keep in mind that if you have a car, you could easily get to Fionnphort on your own (1 1/2 to 2 hour drive) then take the ferry over to Iona on foot. That's what I did and it worked out well.
I would also recommend the Walk Highlands website that Laurie Ann mentioned. That is by far and away the best resource for hiking in Scotland.