It's a good job you aren't into winter sports as most of these places won't have snow much before mid December!
Hallstatt: WHY? Yes it's pretty but so are other places that are much easier to get to! Like Obertraun across the lake which actually has a railway and is the place to be for the caves. Looks not much difference on the map but by public transport it makes a lot of time saving. And if you come from Vienna via Attnang-Pucheim (one station, double name) you'll get the tourist view of Hallstatt across the lake (sit on the right). Or possibly Bad Ischl a few stops back. You mention the Schafbergbahn, this only runs until mid October and only has 2 guaranteed departures (both morning) with more IF the weather is fine. But if you get weather good enough for this why spend time down a cave? And if the weather isn't good enough for them to run the train then going down a cave might be a good idea. Stay in Bad Ischl, do just one depending on the weather. You won't have 2 days anyway, it will be midday before you get there.
Großglockner Road: Is not that far from Salzburg city (most of the road is in Salzburg Land). Unfortunately the Postbus I once rode from that side appears to have been discontinued, only route 5002 from the Lienz in the south to the summit seems to run and their timetable system denies knowledge of it at the download page (but shows it in the specific journey planner!!). Don't worry, there are alternatives to come
Innsbruck: we'll come back to that, your itinery is in the wrong order and doesn't make best use of time!
From Bad Ischl (area) head back to Attnang-Pucheim, then fast train to Spittal-Millstättersee (one station, one name of two words) and on to Lienz (NOT Linz!!!!). Change here to the cross border train and head to Bruneck/Brunico in Italy. Northern edge of the Dolomites. Much of the Dolomites were previously part of Austria until the end of WW1 when the border was redrawn. Within this area German is still the first language but almost everywhere has two names, Google Maps sometimes only shows the Italian version just because it's in Italy, but Streetview shows most of their roads - research and enjoy! The ex Austrian area is known in German as Südtirol (Alto Adige in Italian) and has what may be Europe's best public transport pass, the Mobilcard.
http://www.mobilcard.info/en/mobilcard.asp
It covers all trains except the international Eurocity service on the Brenner Pass line and the high speed trains southwards from Bozen to Rome. Plus all city and regional buses. Plus several cable cars. I think a 3 day pass (at less than €8 per day) will come in handy, but for a longer stay the 7 day version is only €5 dearer so don't worry about wasting a day or so off the end. From Bruneck you can get regional buses south into the mountains and several of the roads are nearly as impressive as Großglockner. Some bus lines may be ending in late September but there must be something worth riding! If you like the idea I'll work out a plan.
From Bruneck it's easy to reach Innsbruck in just over 2 hours. Train to Franzensfeste, quick change for the climb to the border at Brenner. The Mobilcard is valid to Brenner if you have any days left on it. At Brenner change into Austrian train for the short ride down to Innsbruck. Plenty of time to wander around the Altstadt.
Swarovski (if you must...) is easy to reach from Innsbruck, there is a bus direct to the door every couple of hours or regular local traisn to Fritzens-Wattens (two names because it's shared!).
The german border town of Mittenwald is a nice half day trip in dry weather, the old town has painted frescos on the outsides of most buildings, trains every couple of hours.
Back to Vienna. Forget using Munich airport. Innsbruck to Vienna Airport is a direct train ride in less than 5 hours (every 2 hours). Or try an internal flight from Innsbruck
