Hi, Donny,
There is in deed no explanation of what chord 1,2 and phrase 1,2 in PSR9000 owner's manual (version 1 & 2). They only showed these in Track Muting & Volume Control on p.24 and Style Creator p.104 of the version 2 manual (English version).
Despite this, after seeing you post this question, I turned on my PSR9000 and played with different styles and observed and compared these four parts elements of styles and found the following facts:
1. Chord 1 and Chord 2 are riffs of chordal instruments (like guitars, piano or EP) based on chords determined by your chord fingering. These are composed of multiple sounds of chord sounding simultaneously. Most of PSR9000's stock and flash styles have both Chord 1 and Chord 2 voices in the more complicated variations of the styles (like variations C and D), whereas in less complicated variations, like variations A and B, sometimes only Chord 1 or only Chord 2 is present in those variations.
2. Phrase 1 and Phrase 2 are like solo riffs that are based on single instrument playing running solo notes. They may be chord matching like arpeggiator, or rhythmic replay of same pitches, or pitch variations of octaves. The essence of it is one note at a time, not multiple notes stacking at the same time like a chord. There may be some styles that have both phrase 1 and phrase 2 elements, but I have not found many of them. I think that these 2 parts elements are for the flexibility of style creation, most of the styles get by using only one of them.
I hope this little observation may be helpful in answering your question.
Regards,
Paul Ip
from Texas