What I'm doing, rather than recalculating CR's is just rating how difficult or hard it was for the PC's to overcome. If they do it too easily, less XP (as if its PF CR were lower than it's listed 3X CR). If it's harder than it should be, a little more (as if it's PF CR were higher than the 3X CR). I, also, adjust the PF CR's in a similar manner, as PC parties vary in power from one party to another and while the CR system is good, a CR 3 monster might not feel like a CR 3 monster should against a level 3 party, in some cases. So, I might count it as a CR 2 or as a CR 4 depending on the circumstances.
I'm trying to do as little conversion as possible, though, as real life doesn't allow me the time to convert everything. Was originally planning to convert everything to 5E, but it's easier with the volume of 3X/PF material to stick with PF/3X and just convert what I want from 5th.