Well, the idea with “chunking” is to take long complex passages, and break them down into easily repeatable, isolatable, mechanically similar components, so you don’t have to think about the whole passage, just about how you put the “chunks” together.
So, where is the challenge in this run? is the challenge remembering all the notes, and if so, are there clearly defined “parts” you could decompose the run into? Or is it just difficult to execute? I don’t know the particular run you’re thinking of, but if it’s something that DOES have a structure that lends itself to breaking it into parts, and thinking of it in those parts makes it easier to get your head around than thinking of it as a whole, then maybe thay’s an option.
But, my bias here, flying blind, is that’s probably not the case. If you can play the whole thing and it’s just a matter of getting it up to speed, I’d say maybe just slow that line down (I actually use Reaper, with a MP3 codec enabled, for this when tring to learn something complicated), and then play along with it at a slower tempo you can nail the part at, and then gradually speed it up until you’re close to/at tempo.
Someone please check me if I’m wrong, but “chunking” from a picking perspective is a way of taking a fast repeated motif that can be repeated easily and then linking it together into a much longer line, in ways that save you from having to think of all the intermediary notes so much as where the chunk starts and where it ends, and how you move to the next chunk. That’s probably not a description of what Vai’s doing in this line… but I could absolutely be dead wrong!