Why did it take nearly 100 years after the ratification of the Fourteenth Amendment before suspects charged with crimes at the state level were afforded most of the same due process protections as people charged with crimes at the federal level?
The answer to this lies in the federal judiciary's interpretation of the Fourteenth Amendment. Nowhere in the Fourteenth Amendment does it state which due process of law rights are meant to be provided by the states, and each of the various rights had to be litigated up to the Supreme Court to get rulings on the due process rights that are enumerated in the other amendments. As your question notes, not all of the rights have made it under the fourteenth amendment, including the right to a jury trial for various matters in some state proceedings. The right to one's Miranda warning did not emerge until 1966. If you can picture the Fourteenth Amendment as a door, the intent of the framers was probably to open the door to every single enumerated due process right in the other amendments and apply it to the states, but in fact, the door was only open a crack initially, and it was only with each due process right being litigated that it became almost entirely open.
We need to remember the historical backdrop for all of this. The victors created the Thirteenth Amendment to free the slaves. The southern states responded by creating a two-tiered legal system that made African-Americans second class citizens. The response was the Fourteenth Amendment. The southern states were by no means ready to give up their way of life at that point. As a result, as each due process right was asserted, the response of the southern states was, "Well, Your Honor, that right is nowhere mentioned in the Fourteenth Amendment." So, you can see it was hard going, and each right that now comes through the Fourteen Amendment door had to be fought for.