I did this in October while on a Highland Rover just before the summer timetables finished.
The train into Kyle was late (which the guard said isn't uncommon) so I missed the 51 bus which leaves shortly after it gets in and got the Citylink coach up to Portree instead (12.15 I think). It is a beautiful run up there, some stunning views.
The fly in the ointment was that it was windy and for the first part of the day the ferries from Armadale to Mallaig weren't running. Having seen the forecast I knew the wind was due to die down and they did start again in the early afternoon but on 'amber alert', meaning they were liable to short notice cancellation. A couple of calls to CalMac and they were very non-committal, but in the end I risked it - the only alternative was to shell out £30-odd for the Citylink from Portree all the way round to Fort William (I had a hotel booked in Mallaig so would have then had to wait for the late ScotRail train). This shows how Skye relies on that one road connection at Kyle!
I got the 15.40 bus from Portree (which only runs in school holidays IIRC) which was actually a coach with disappointly filthy windows and 3+2 seating, but was fine, we kept time comfortably and as we approached Armadale I could see the ferry on its way across. I even had time for an ice-cream from the little kiosk before I boarded (there is nothing else there at all). There was one car and about 4 or 5 of us foot passengers! The crossing was very pleasant, I've not been on many boats but I've definitely had worse crossings than that! The ferry comfortably connected with the train - I walked across to see it go before finding my hotel.
Oh, and kudos to the Citylink driver who was incredibly helpful (he drove the coach I took from Kyle to Portree and then went on to Uig and back, so it would have been him I would have been with if I'd gone to FW by bus) - he knew the timetables off the top of his head and reassured me that if I ended up at Armadale and the ferry wasn't there I would still be able to make it round somehow, although I'm sure it would have been very expensive!
As for the last question, you're right, the trains do cross at Ardlui and its an island platform so not even a footbridge to cross. If the Up train is late it might wait at Crianlarich instead I guess. You could get out and wait at Crianlarich but there really isn't much there and I doubt the station tea room will be open at 7.30 in the evening!