The Mallaig-Armadale Ferrydoesn't run through the winter and usually stops as the Scottish October school holidays finish which this year means 21st October - in other words the day before Dogdogman's holiday starts. Also, given that Glenelg isn't that easy a place to get to you don't want to arrive there and find the ferry isn't running because the only way to then get on to Skye is to retrace your steps back over 10 miles of mainly single track road and then continue on right round Loch Duich to Kyle of Lochalsh and use the bridge.
Please note too that this is a privately run ferry that was up for sale and a local community buy-out wasn't successful. Before committing yourself to this route it would be best to check before starting out that it will still be running in late October or at all. Much to the annoyance of many English visitors many summer-only ferries stop the weekend the English half-term holidays start! And of course don't get caught out by confusing a place name with the existence of a ferry! There always used to be a ferry that crossed Loch Carron that saved visitors a massive detour round the sea loch but it has long closed with the result that now the signs on the main road pointing to the village of Strome Ferry have 'No Ferry' in brackets underneath them!
You don't say where you are starting off from but I would agree with others that driving up to the West Highlands for just three days before driving back down to Edinburgh is a very hectic schedule. Most of the 'A' roads are still going to be only single carriageways with at most the occassional few miles of dual carriageway to allow the queues of traffice to overtake the caravan or tractor holding everybody else up. And many of the 'B' roads are going to be single track with passing places.
I love Skye and think that if your daughter is into wildlife eg otters etc or history then there will be plenty to do to keep her entertained but I would leave that for another trip and consider spending some time on the way up to Edinburgh. For example if you are travelling up the M6 then Dumfries and Galloway is lovely and there are all sorts of attractions that might be of interest. On the other hand if you'll be travelling up the east coast on the A1 then Northumbria and the Scottish Borders have just as much to offer. Given that you only have 6 days I wouldn't bother driving much further north than the central belt, ie Stirling, the Trossachs or possibly Tayside. And if you really do want to include an island in your trip well think about Arran as a possibility. Much easier to get to than Skye and very beautiful too.
I think that one of the things to bear in mind is that less than 10% of the UK population lives in Scotland and the majority of them live in the central belt ie greater Glasgow and Edinburgh and the commuter towns inbetween. The rest of us are then spread very thinly around the rest of the country and almost anywhere outside of the central belt is going to feel very rural and uncrowded compared to England but the standard of the road network reflects this too and 50 miles in the highlands will take as long or longer to travel than 100 miles elsewhere even if there won't be the same traffic jams etc. And all the other facilities are similarly spread out too. If you go to Skye and it's wet then a trip to the cinema will involve something like a 200 mile round trip because the nearest ones are in Glasgow and Inverness!
SM