This is some amazing stuff that I've spent a tremendous amount of time on over the years. This IS the matrix of ratios...only here Vai is explaining how Zappa (and many 20th century composers) took it futher and further and further. An amazing topic really. HUGE books could be written on this subject.
Pebber would probably say to get the easier stuff down first! Drill groups of 5's and 7's and 9's on one string with a metronome. Get that down really good first.
But to answer your question, what Vai is talking about is the matrix of ratios only expanded out further and further into more complex territory.