aye, strings too high is one thing that can cause intonation problems(they need to be quite high though), the other aspect is string length, each string needs to be the correct length, that’s why you have those screws on the saddles of the guitar to move them back and forth. (If you don’t have them you’d need a custom bridge.)
Normal guitar setup involves 3 basic aspects(there are more, but these are the important bits): Putting a bit of relief in the guitar neck; Setting the string height; Properly tuning the string length. (you do use an actual tuner, and tune the 12th fret on each string, bit of a heid*** especially on a floating trem).
All easy enough if you’ve spent 6 months pissing about with yer guitar setup learning how to do it! 😆