Dear Daniel,
Yes, in your plots, you still see protons because they are not drastically removed from the simulation. Instead, they are ranged out to rest in an approximate way (as noted in the manual under Note 4, PART-THRes card, which you have already identified).
Based on what I see in your input file, I believe that adjusting the protons production thresholds would surely affect the physics of your transport problem.
This thread (and related links on the page) offers some considerations about a similar issue and may help provide an overview. In short, handling this in a detailed way would likely require advanced user-written routines, possibly intercepting the secondary particle stack (introduction in this advanced lecture).
Depending on your needs, another option would be to adjust the scoring. A straightforward approach could be to set different energy ranges in your USRYIELD cards or filter particles below a certain energy at scoring time using advanced scoring techniques, such as fluscw.f ).
A side note about neutron transport:
- PART-THRes: the energy threshold is in GeV. Currently, your neutrons have a cutoff at 1E-5 GeV, but you might be interested in the full transport down to 1E-14 GeV.
I hope this gives you a good starting point.
Best of luck with your simulation.
Tommaso