(1) I've found some inexpensive bus tickets for this.
(2) I'm mostly having trouble here. I see shuttles that go direct for about $130 for two. I've pieced together trains going CK, to Ceske Bud, to Vienna for about $80. I'm thinking this can be done easier or cheaper as the Gmund to Vienna leg is coming up at 48 euro. Other option is shuttle to Linz, but the train to Vienna is coming up at 53 euro. Is it possible to buy the 28 euro Einfach-Raus ticket going into Vienna? Is it something you need to purchase in advance?
(3) Seems pretty easy. Trains run during the day, just buy a ticket at the station? I've seen some posts saying as low as 14 euro?
(4) Not sure about this one. Hard to find any info on pricing. Any help would be appreciated.
...all the way to Wolfsthal near Slovak border. From there, you can take bus Nr 901 to Bratislava. The ticket price is 1.50 EUR per person (or 0.75 EUR for those younger 26 years).
If going one-way I prefer connection via Komarno/Komarom as the stations Sturovo and Ezstergom are quite distant from each other (approx 6-7 km). Sturovo station is located out of the city and it is better to take the bus to get to the city proper. Komarno - Komarom distance is no more than 3 km.
However, as for the price on route Bratislava - Budapest, no one can compete with buses of the Student Agency company, with prices starting as low as 5 EUR (but more realistic is 7 EUR)