A) By best do you mean fastest? I’ll try to spend some more time o this later, but Option 1 seems to involve less total time on the train — my choice, although there isn’t much difference overall, so I’d probably go for whichever works out cheapest.
B. I didn’t find good prices either. Since the most direct overnight route involves a connection in Munich, does changing your route to Berlin-Munich-Vienna-Innsbruk-Zurich work? That takes advantage of a cheaper Berlin-Munich overnight for your date.
C) This one takes more map and schedule work than I have time for right now…..

By best choice I just mean.. well, I guess nicest route? I’m not too concerned about time because its going to be the same amount either way so I guess nicer train ride? Going to decide by next week, might end up just going to Munich from Vienna and then doing a day trip to Innsbruck or something like that. Or go from Vienna – Innsbruck just for the day then take last train to Munich also.
Unfortunately it wont work because the dates we have planned we want to be in Munich for the weekend to see friends (they’ll be busy during the week).

Austria has a group travel ticket for 31 euro a day which covers up to 5 people. Germany has a similar ticket (the Bavaria ticket) which will get you from Munich to Innsbruck and back (check this, we went from Munich to Salzburg on our trip, but my recollection is that Innsbruck was also an option).

I think the economics argue for Vienna to Innsbruck, then Innsbruck to Munich, but the tickets are so reasonable the economics are not a big factor. I think the Austrian ticket is for second class, but I know the Bavaria ticket now offers a first class option, at higher, but still very reasonable cost.

I found a day tour (+trip to Swarovski world although not interested in going there hah) from Munich for only 50$ which will save a bit of money than taking the train to/from Innsbruck (+maybe hotel/hostel for a night). So maybe this way to just go Vienna – Munich and just stay there an extra day/night (instead of Innsbruck..).

If it is worth it to stay a night in Innsbruck, then which would be the nicer train rides (for those who have done them); Vienna – Innsbruck, Munich – Innsbruck, Innsbruck – Zurich. Like Cleveland said the economics are pretty much the same so I’m just looking for the nicer train ride.. I imagine Innsbruck – Zurich would be quite nice. I’ve also gone from Zurich – Munich before its nothing too special which is why I’m asking about to/from Innsbruck..
All suggestions & input are welcome. I find I keep changing my mind or finding other random places that look beautiful which would all be nice to see (Mittenwald for example) but don’t have the time for, heh..

Last option I was considering is going Vienna – Munich – Seefeld for a day – Zurich via Innsbruck..

Thank you again for the quick replies and great input!

NONONO!!!listen here, the best route ever is only in Argentina. It is called route 40, it goes through the whole country. And if you are at all familiar with Argentina you will surely appreciate the craziest journey through its golden beaches, high Andes, cold patagonia and beautiful Mendoza. It starts at the zero km in Bolivia and ends in the most southern city in the world Ushuaia^)Gosh!it is simply thye best))