my suggestion is to use a skeleton-edition style case so you print the minimum amount needed, and reuse the base plate. ie print only thumb plate til you get the position close, etc.
I've build a framework for this approach: https://github.com/wolfwood/tryadactyl
trying to link the keyboard parameters to measurable features of your hand helps some, but honestly there's no substitute for typing on it and realizing what you don't like :)
i've has a recent breakthrough (implementing hierarchical/delegated column placement) that makes merging multiple plates with differing centers of rotation just work when switching from an open case style to a closed case.