Please, is there a collective word for all the parts of a word, prefix, stem and suffix?
Word part would be the only phrase that can be considered as a hypernym for all parts of a word. (Some sources mention as word element also).
If you didn't say stem but said root, morpheme would be the collective word. Because roots are composed of only one morpheme while stems can be composed of more than one morpheme. So we can't say that all stems are morphemes.
But some sources still mention stem as a morpheme because they can be roots or inflectional roots.
In general, morphemes are affixes, roots and clitics.