Hi again, Linda,
I'm not sure that the boat tours to Staffa will be operating in mid to late October. You may want to contact one of the tour companies (Staffa Tours?) to find out. You can, however, visit Iona. The passenger-only ferries depart Fionnphort several times a day. However, if you are staying on Iona, you don't need to worry about the ferry schedule. Boats to Staffa leave from several places on Mull, including Fionnphort. Iona is very walkable. There are no steep hills.
You didn't say how much time you have in Scotland. Daylight hours will be getting shorter as you near the end of October, which may curtail some of your plans. However, there is still lots to be seen.
Given your sister's mobility issues, I'd say that since you'll have a car, a rough itinerary would be as follows:
Edinburgh to St Andrews. Visit the castle and the cathedral.
St Andrews to Dundee: Visit the RRS Discovery and view the introductory film
Dundee to Aberdeen: Take the coast road. Stop in Arbroath for smokies, a local fish based delicacy. Visit Dunnottar Castle, just outside of Stonehaven. (Your sister will not be able to make the trek down to the castle, but all of you can enjoy the magnificent setting from the car park.) Outside of Aberdeen, visit Crathes Castle (open Thursday to Sunday in October) and Fyvie Castle.
Aberdeen to Inverness: Take the coast road. You can enjoy some of the charming fishing villages along the Moray coast, like Pennan, Portsoy, and Cullen. Enjoy some Cullen Skink (a delicious fish chowder) in the town for which it was named.
Inverness to Fort William: The A82 follows the west shore of Loch Ness. There are a few viewpoints along the way. You could stop at Urquhart Castle. It's relatively accessible for visitors with limited mobility, so your sister should be able to enjoy her visit.
Fort William: In mid to late October, the Jacobite only goes out in the morning, so that would involve spending the previous night in Fort William. You could take a drive up Glen Nevis to get a closer look at the "Ben"; however, the best views are from Corpach on the A830.
Fort William to Skye: You'll be retracing the train route that you have already taken, from Fort William to Mallaig. From Mallaig, ferry to Skye. As you noted, most of the hiking on Skye is going to be beyond your sister's limitations. However, there is still plenty to see that can be seen from the car, or a short level walk from the car. A lot is going to depend on weather. If it's overcast with low clouds, you're not going to see a lot. On the other hand, if it's one of those sharp clear October days, as frequently happens, you'll see a lot!
Skye to Mull: There are two ways to approach this - The most scenic would be to take the road from Inverailort to Kilchoan, then the ferry to Tobermory. However, the winter ferry schedule goes into effect on October 23rd., so you may be looking at a more limited availability. The same goes for the Mallaig to Armadale ferries. Once you arrive in Tobermory, it's a straight shot down the main road to Fionnphort. Your second route would be to retrace your route to Fort William, then follow the coast road down to Oban for the ferry to Mull.
Okay, that's just a basic outline, in conjunction with your previously stated plans. There is still a lot more to see and do, including Stirling Castle, Aviemore, the Queen's view of Loch Tummel, Falkirk, Dunkeld, etc. And that's without even touching the Highlands proper.
But I hope that I've at least provided you with a start to your plans. You may want to spend all of your time in Scotland and skip Ireland altogether!
Very best wishes,
p.s.: Glasgow deserves more than a day trip. You could spend a week visiting all of the excellent museums and historic sites in the city, almost all of which are free.