Need some recommendations on organizing data
Using a surrogate key as a primary key for tables is a very common approach and it seems to fit your situation quite well. The foreign key in local maxima can then be a single column referencing the surrogate key.

If the relationship between the definition of the run and the outcome of the run is a one-to-one relationship, then you should at first consider having them in the same table, and only split them up if you feel it's more natural, convenient, or better for performance.