First off @severedsolo I absolutely love your mod due to how its changed KSP for the better in career mode. With only 500hrs in this game this mod has singlehandedly reignited my love for KSP. I love 95% of the systems you have in place with this mod.
Have you considered though that instead of science experiments providing science points into the pool for research that they would instead provide reputation(maybe 1/10 of the amount). With rep decay on by default(anti runway/cheese mechanic), your budget is influenced more by how much kerbin notices your recent scientific achievements than how many experiments run to unlock more tech. It shifts the focus more to how great you are as a space faring nation(rep) than how much can you cheese the science system. As a direct result your R&D center would now provide a monthly science award based on something like (science budget*x) where x is your difficulty multiplier. So basically your nation is providing monetary resources(based on rep and budget amount) into developing tech to reach the stars. I think this would provide a more organic tech progression than relying on spamming boring science grabs just to jump the tech ladder. So if a player was to get stuck this would allow you to take a rep hit to get that next tech to go where you want to without the whole, ‘What biome in minmus havent i stripped of science yet’.
To balance you would have to lower the rep payouts of contracts and could even go as far as creating a win/lose condition to career. 0 rep = kerbin doesnt want to fund space exploration anymore because its too hard. Max rep = You have created the most prestigious space program kerbin has ever seen.
Im sure you have thought of this already but I figured incase you havent, maybe something to consider for future development. As im not really a coder or modder I am not sure the technical limitation of ksp and the systems they have designed could even accommodate this....