Good 
As for Assistants or GPTs … I only use the API with the “raw” models (GPT-4/3.5), without any thin-wrappers from GPTs or Assistants. Maybe others can chime in on that transition, if there is confusion after reading the docs.
But you need to transition to fine-tunes, which is like using raw API models without the thin-wrap.
So to keep everything on the same level, just use this “raw” model family IMO.
The only exception is maybe the RAG part, where you might be inclined to use Assistants. So maybe do that. But I would quick spin up my own RAG if I were you, to gain more control of the overall system.