Train or Bus Travel between Villshoffen, Germany, Regensburgh and Prague

There is a direct train from Regensburg to Prague every 2 hours and it takes 4 hours.

To get from Vilshofen to Regensburg, you need to change trains in Plattling. Not a big deal.

The Flixbus takes about 3:30, the train about 4:00. But on the bus you are locked into your seat the whole time, while on the train you can walk around (the train is rarely full beyond Regensburg). If you take the train, be sure to book your tickets with Czech Railways (www.cd.cz), where they are much cheaper than with DB and also include a seat reservation. However, seats are usually only allocated around 4 weeks before the start of the journey, so you shouldn't get nervous.
Bring your lunch aboard, there is only limited offer of food.

Thank you both for such useful and helpful information.
www.cd.cz looks very easy to make a reservation in English for the train from Regensburg to Prague.
Is a second class ticket adequate or would we be wise to pay significantly more for
a first class or business class ticket? Is there an advantage to booking now for a
November 8 travel date?

Regarding Vilshoffen to Regensburg: what is the website for booking? Should we book now for November 6? Are tickets cheaper if booked ahead of time?

Thanks again for all your help.

Is a second class ticket adequate

Yes. I would never buy a first class ticket for that train. First of all, it usually only has 24 first class seats (more only are added in Plzen), so it could be that there is little space in 1th class.
Secondly, it may happen that there is no factual difference to first class because the first class compartments are usually in a wagon of the (Bavarian) Länderbahn, the 2nd class wagons of which often consist of downgraded Italian first class wagons (the parent company of the Länderbahn is the Italian FS). You can see a layout of the train leaving Regensburg at 10:17 here: https://www.vagonweb.cz/razeni/vlak.php?zeme=%C4%8CD&kategorie=EC&cislo=355&nazev=&rok=2024 ((please note that the first two carriages are only attached in Plzen).

Is there an advantage to booking now for a November 8 travel date?

No. As stated above, usually the CD is starting its free seat reservation only 4-5 weeks in advance. So, if you want to take advantage of it you have to be patient. Try it again and again from the end of September and on day it will work.

Regarding Vilshoffen to Regensburg:

(1) what is the website for booking?
(2) Should we book now for November 6?
(3) Are tickets cheaper if booked ahead of time?

(1) https://int.bahn.de/en/
(2) No, that's local transport without a booking deadline and without a seat reservation
(3) No

And travel after 9 am and the cost is 39 EUR for 2 people with a Bayern Ticket. You can buy that from a vending machine in Vilshofen station on day of travel.