As I stated most are educated guesses, but some of it is from educated taste buds combined with a love of history. What would that drug store in Waco have available at the time?
Sarsaparilla and Sassafras for sure as they were used in many medicinal formulas. They were also used in root beer, both the alcohol based type and the non-alcohol type. Doesn't Dr Pepper seem to have strong root beer component to it? I think so. Yet it is more complex.
Some things I just taste, like the nutmeg. Nutmeg has been used for centuries as a very powerful drug. I assume a drug store of the time would be well supplied with extracts of it.
Certain almond extracts can give a better taste of cherry than cherry itself...manufacturers still take advantage of this fact to this day. That's why I think almond is in.
Kola nut. A primary source of caffeine at the time and obvious. Although the original formulation was simply called a Waco and not called Dr Pepper until later, I do think it had a "pep" nature to it as most later soft drinks did.
Fruit juices: A few I can taste, but some I assume as being available. Dr Pepper has always branded itself as a blend of fruit juice flavors, but I think there is more to it than that.
I think we will always wonder what the original Dr Pepper tasted like as there is nobody alive that ever had one. I am sure the modern version is different and modern methods are used to try to recreate the original creation.
I am still interested in other thoughts on the matter...right now I have only half a list.