When you buy your ticket, ask for Nam Tok. You can only buy one way at the Kwai bridge ticket office. I think you can step off at Tham Kra Sae then jump back on the next train to Nam Tok. You may have to start on the early train to fit it all in with the train schedule. Hope this helps and safe travels. Strangely i am currently watching the River Kwai movie at home. Lest we forget

I have no idea if there would be a bus from Mallika through to Krasae but even if there was it would probably still drop off on the main road (some way from the railway). Although I might be wrong your second option of going back to Kanchanaburi seems impractical. I have little doubt there would be options available from local travel agents in Kanchanaburi that would take you on a minibus to these places, returning to Kanchanaburi on the train from Tham Krasae. If you are determined to use the local bus then the best option might be to get a taxi from Mallika to Tham Krasae station and catch the train back to Kanchanaburi.

We stayed for two days, went to hellfire pass museum followed by death bridge, onto Sai Yok national Park for river rafting, there is another national park with a waterfall Erawan, then Hindad hot springs, there also plenty of other museums about if interested in war memoribilia. But if staying in Kanchaburi seek out the Loft as it is a fantastic restaurant.