For information on the transition from the DST root to ISRG's own roots, check out this blog post:
When talking about what specific roots you want to put in a trust store (while I think that ISRG Root X1 & ISRG Root X2 are likely excellent choices), I think you need to start with a bit more detail on why you're building your own trust store rather than relying on a platform's built-in store. Maintaining a trust store is a generally a long-term commitment as roots change over the years, and occasionally roots need to change on short notice (if a key is compromised or an organization turns out to be untrustworthy).
You might want to read through this thread of some things to think about when embedding a trust store in devices (which might not be your use case, but this might be enlightening anyway):