I was wondering if there are any other options/tricks I could explore? Can anybody offer some advice?
Actually you can buy same 39 euro ticket already from Kittsee/Marchegg, thus saving on route to Vienna.
On DB website there is as well 29 euro tickets available for Breclav-Stuttgart connection (11:02-21:28), but those involve bus ride from Prague to Nurnberg. Bratislava-Breclav is cheap and easy.
Also, am I right that the return tickets from Bratislava to Vienna are only valid for one day after they have been stamped (I know that its one month unused)
Hmm... we never heard about such thing, it sounds a little bit suspicious. Maybe you mixed it up with one day validity for Vienna city transport? Because minimal validity period of similar international ticket is usually at least 4 days, which not depend on stamp when you go there.