Looks like I got a little late.
My name is Alexandre and I am also from Brazil and I know how hard is to get good stuff here and how high the costs are.
Since you already have the saddles there's not much thing to say, but that I would consider to get phase 2 locking tuners or the Planet Waves autotrim. The Planet Waves one you can get here and the Phase 2 you can get at the PRS Store.
About the intonation, since you mentioned you already did what you sounds like the right thing, I would recommend to check with a tech. IF you tell me where you are I can check if I can recommend anyone to you.
Took the guitar to the tech, now it is perfect! The 3 thinner strings have the TUSQ saddles, the 3 thicker the original saddles. Looks different!
I don't miss the locking tuners, my guitar isn't detuning at all...
Sounds great! I've just had phase IIs put on my CU24 and 59/09 and Dragon II pups. It sounds & plays incredible now! No tuning issues at all & I still have the SE nut. I think a lot of so called tuning issues are down to strings not being properly stretched.
Next up - I think the US lampshade knobs will finish it off nicely :-)