Chicken Lover - I visit the Wachau routinely and think you are making a great decision to stay in the area for 3 days. October will be a nice time, not too cold, not too hot (hopefully). You will likely have missed the grape harvest but you might be lucky and find some sturm still around.
For your trip you will rely on buses, not trains. The WL1 and WL2 bus are all you need to know. The WL1 bus runs from Krems to Melk on the north side of the river; WL2 runs on the southside, also from Krems to Melk. Bikes are not allowed on these busses typically. There is a special WL1A Radtramper, which runs until Oct. 26 and is specifically for bicyclists. There are several ferries along the way where you can cross by small boat.
Here is the link to the WL1 schedule:
I am glad to see that you are asking about the south side of the river. Most visitors, especially those coming for the day, focus on Duernstein. While it is a lovely village, it is becoming increasingly full of tacky tourist shops. That said, you must have lunch on the terrace of the Richard Lionheart Hotel and you must hike to the castle ruins above the village where Richard Lionheart was imprisoned. I actually like to stay in Duernstein at the Gasthaus Stoger.
Weissenkirchen is known for excellent wineries and good restaurants. There is a ferry at Weissenkirchen that will take you and your bikes to the village of St. Lorenz. From there it is a lovely walk/ride to the next village, Rossatz. An smooth, uncrowded trail runs along the river (far from the road) through vineyards where you can have excellent views across to Duernstein. Nice picnics spots.
You should also investigate the Aggstein castle ruins, visit a winery or two (WEINGUT JOSEF JAMEK, WEINGUT PRAGER, WEINGUT HOLZAPFEL, WEINGUT KNOLL).
To get back to the train question, there is a special tourist train which operates between Melk and Krems, but it only runs for a part of the year, only on the weekends and holidays and only runs 3 times/day. Bus is way better.