Have you thought about the idea to motivate players with blockchain tokens?
Value of the tokens can be bound with licensing usage of research result.
Non-profit does not mean no money involved as long as we are solving the right problem.
But I'm not sure it's not contradictory with the reward model of Foldit: "non profit" and even, for most of the players, no reputation (using anonymous pseudos). One can be anonymous and be self-satisfied to contribute to science (by making the first designs) ... or simply to "gain" as a player (by gaining the final sprint).
May be the same game could run in parallel with blockchain tokens rewards, capturing other player's types, I don't know.
In practice, I suspect it's difficult to measure the contribution of each player to a solution, whatever the method. For example, the point jumps are not necessarily related to the final result (a negative point is often associated to most valuable hand fold contribution). The total ranking is not necessary linked to scientific results: for some published papers, low ranking temporary players contributed significantly. Skills and experience are useful, luck as well.