I used to "measure" the relief and action with measuring tools but about 20 years ago realized the "suggested" parameters are just that, suggested.
Getting the action low is a multi-stage process. A dance between relief, string height, fret buzz and choking as you describe. I have two PE-R80s only 2 years apart yet the relief and string height are different for both. I start with only a very small amount of relief and lower the strings in small steps until I get a distinct buzz then raise the the strings one step and play it for a week or so until things settle in. Sometimes I have to add a little more relief and others I don't.
It is important to give these old guitars some time to acclimate in between changes. New guitars have not "settled in" and react quickly to changes but these old guitars have and changes happen more slowly.
No two pieces of wood are identical and as such no two necks are identical. The difference may be minute but if you're like me you can "feel" the difference.
With regards to string rattle three things come into play. How "lively" the neck is and string gauge are two. On my 25-1/2" scale guitars I run 10s but on the 24-3/4" scale guitars I run 9s. The last thing is a trem. Believe it or not a floating trem can add string slop to what would otherwise be a stable action.
The fist thing to tackle is relief. As little as possible yet enough to avoid string rattle on the first few frets. A neck with a lot of relief but low action is more likely the choke on the upper frets.
One last thing to consider is the clamping a pickup's magnet has on the strings. If the magnetic field is strong enough it can change a string's vibration dynamics. Believe it or not a string vibrates from end to end back and forth. Many moons ago I had a strobe light in my room and one day noticed that the string vibration was not spread across the entire string but it had "waves" that went back and forth from one end to another. If a pickup's magnet is strong or it is too close to the strings it does change the dynamics of this moving vibration or waves and can actually cause string rattle as well as intonation issues.
For reference:
https://www.youtube.com/watch?v=8YGQmV3NxMI