This is quite a hard case, because it's your Mum, on what I'm guessing is likely to be her only trip to Scotland. So some, or a lot, of the usual advice has to be adapted.
Personally I'm disappointed for her if we can't manage somehow to get her to Skye (and sensibly that means Inverness). But if that boat has sailed so be it.
Sticking to what is suggested above usually the choice of tour would be clear- Stirling, as opposed to Loch Ness.
In this case I'm really, really not sure, is your Mum up to 12 hours on the bus with several stops? If so my gut feeling is that Glencoe and Loch Ness is the one to do. The Loch Ness stop is at Fort Augustus. Unless the boat trip is on the fast RIB I don't think it can get to Urquhart Castle and back in 50 minutes- for better or worse, and it looks like the bus isn't going up there either.
The positive is that Fort Augustus is a nice wee village, the Caledonian Canal is especially attractive there, and you can see a long way north on Loch Ness.
So I think that gives a very good taste of the Highlands.
To Fort William there is only the Scotrail train. While I'm firmly in the anti Jacobite train club, if it is running by then then yes, why not. And I'll go further for this one case (it truly is an exception) and say spend the extra money and go first class, because I want this to be as special and memorable as can be. Yes I do know the 1st class food and beverage offer is rather tokenistic (I've done it, being a miser I felt just a bit cheated). If the Jacobite isn't running then just the normal Scotrail train.
The Loch Shiel cruises are a great idea, logistically they are not that easy to make work without a car or staying overnight at Glenfinnan. You used to be able to go one way to or from Acharacle and bus the other (I've got that teeshirt) but the bus has stopped.
I also think you need 2 nights in Fort William, due to the timings of the Jacobite steam train.
Bear in mind this is October, there is a real chance of ferry disruption so I would want to have at least two full days in Oban to give the best chance of success. I'm not sure the south end of the Isle of Kerrera walk is suitable for her- but the north end with a meal at the Marina is (if Mull/Iona was unviable due to weather).
Yes, the wait between trains at Crianlarich is about an hour because the two trains (north and south) pass each other at Ardlui (closer to Glasgow), so the bus is always faster. The pro tip on a fine day without luggage (and a bit younger) is to get off at Tyndrum Upper and walk down the hill to Tyndrum Lower!
You won't be able to book train tickets until 12 weeks out, so sometime in July. Book through Scotrail due to their split ticket feature.
If and when the Jacobite opens for booking you will probably need to move faster than you do for the Anne Frank House or the Ceremony of the Keys due to pent up demand.
I think Fort William first, then Oban, is the way to do it simply because Oban has twice the train service Fort William does.
PS- the Fort William to Crianlarich part of the line is stunning, as is Glencoe, another reason to do the Loch Ness tour. You really need to do both train and the road through Glencoe, especially if we can't make Skye work.