I don't think the marbles analogy is at all relevant. We are discussing how extremely sohpisticated bits of cellular machinery were put together by evolution. We have the ability to sequence genomes of all sizes from large to small. So in a sense we at least have a rough history of what happened to the 'marbles'. This has not aided in our detailed understanding of how complex cellular pathways were built by evolution.
We can only analyse the genomes of species living today. To exactly know the evolutionary history a certain trait, one would have to be able to know the genome of past species.
Regarding the alps we know the basic mechanisms by which the peaks and dents occur. So what? How does this detract from the fact that we have no clue of how even some very basic yet complex pathways were built by evolution. According to how the current theory stands the probability of a lot of these complex pathways being built by evolution is very close to zero.
We know how blood clotting and some other mechanisms evolved. And we know the mechanisms that are at work. We know how mutations can influence the work of the genes. We know about gene duplication. We know how genes are activated and deactivated. We know all the mechanisms.
The examples of the Alps or the marbles are very apt. Just because you can't explain a certain complex instance of result, doesn't mean the mechanisms you know so far are wrong.