well, i can only half answer the question. effort is calculated and applied at cycle time - whatever bonuses, modifiers or whatnot, that were in place at calculation time, are not going to be re-calculated later. so, if you do effort on C prestige, most certainly this will not be retroactively 'updated' should your prestige improve later. same with changes in preferences.
there is an open question about whether the prestige change actually impacts RS2 recruiting. i would say the default answer is yes, but it has been questioned by some folks and never conclusively resolved. although i do believe seble weighed in and said that the prestige change after the NT should definitely be in effect for RS2.