You are right to point out that giving clear instructions for a complex task is difficult. And elsewhere in this thread, 'nycticorax' makes some great points. I fear my answer is along the lines of Rutherford's often ridiculed quote about statistics and experimental design: "If you need to use statistics, then you should design a better experiment."

If the experiment that you describe in your paper is too difficult for others to reproduce, perhaps it shouldn't yet be published as a paper? Would the public interest be better served by funding researchers who do simpler but reproducible work, rather than complex work where the results essentially need to be taken on faith? Carried to the extreme, this is a terrible rule, but I feel there is a kernel of truth to it.

I guess the right strategy depends on how much faith you have in the correctness of published results, evaluated solely on plausibility and the reputation of the researcher, and thus how much value there is in a conclusion based on irreproducible results. I think there is a currently a justified crisis of belief in science, and that many fields would do well to get back on to solid ground.

But it's a wicked problem.