While there are severe short term problems on the Mallaig to Armadale route passenger charter services are running after a fashion, and the hope is this should all be resolved by the start of June.
So foot passengers can get over currently, with a bit of patience but drivers are really struggling.
Thus I'm mystified by where you have the information about no service on 7 September- I'm not seeing that- 10 September is a single vessel service due to planned ship maintenance, and 11 September is a tidally amended, single vessel service.
To be on the morning train from Mallaig to Glasgow for Edinburgh you would need to be on the 0830 ferry from Armadale.
The next sailings are at 1130, 1310 and 1450 to connect with the afternoon train.
You don't say if you will have a car while on Skye to off rent at Armadale, but if not the 1130 sailing is the one you want, connecting with the bus from Portree. That way you will be able to see the steam train at Mallaig (if it's running) before your 1605 departure, arriving at Edinburgh at 2234. The last hour or so after roughly Arrochar will be in the gathering darkness of night.
Do you know if the Armadale office would be open early enough to off rent a car at basically 0800?
Unfortunately, unless the bus waits for the late ferry you will just miss the 1210 service bus to get to Glenfinnan to see the afternoon train there if it runs.
I think the original plan might have been better, but that ship has apparently sailed, so to speak.
It may be best to have a Plan C in your back pocket, for if the ferry has to be cancelled due to bad weather- namely take the 0800 Citylink bus from Portree to Fort William, then the 1218 train to Mallaig, then return on the 1605 train (the same train set) all the way to Edinburgh.
