If I’m playing long difficult passages like the intro to Cliffs of Dover, my brain for what ever reason seems to get lost with what’s going on, and because of that my picking and mechanics fall apart. Is it because I’m thinking of the intro as one long unit of notes and it’s too much for me to process? If chunking is just visualizing little sections at a time how does that change things with my picking syncing up? I’ve tried to do it I guess, but my mind starts going back to seeing the “whole picture” and because of that it almost becomes a blur. Thanks for any input.
Chris Broderick explains it at the 17 minute mark (I can’t post the exact time since I’m on the cell phone right now), although he refers to it as “fragmenting” instead of chunking. Also check out his tip before that about playing the lick slowly and watch how he chunks the run from one of his songs as an example (even though he does not mention it yet until a minute or two later). Hope this helps!
EDIT: I’ve just realised how late my response is. I chimed in because it was among the suggested topics below the one I started.
I don’t know if this will help anybody else, but I’ve switched over to ONLY playing with a metronome or click track, and I try to tie whatever it is that I am working on to the clicks, so there are “anchor points” of sorts to make sure that I’m not ahead or behind; in other words, I know “at this downbeat there might be a string change,” etc. I don’t really care about most individual notes, because they’re in-between “important” notes that get pinned down very accurately via the clicks. So even if I have variability in my speed it is bracketed over a relatively short amount of time (the next “important” click) so I cannot drift too much.
I know for sure that my brain cannot really process individual notes at even moderate speed, so I have to “let go” and only worry about the “important” notes/clicks.
Does this even make sense? 
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That’s a pretty good nutshell description of chunking.
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I would say that almost any mechanical activity works that way. For example while we’re walking we don’t think about angles,muscle tensions, distances. We just think ‘I want to step there’ and then learned skills reveals themselves. Chunking )
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You’ve got to understand it a little bit at a time.
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Chunking is a lot more difficult than Troy makes it out. It’s hard for me to separate the note groupings in my mind when I play through a long passage of notes. It starts becoming a blur and the notes all just run together. It’s all been such a incredibly slow process. 
It makes perfect sense. Thanks for the tip. 
Play slow to a click (40 bpm) in order to memorise the lick and pay attention to the tempo and the value of each note you’re playing and accenting those on the beat. I’d suggesting practicing each chunk of the lick separately in small doses, and then trying to tie two chunks together, and then gradually add others. What I do in those cases is play a chunk and play the first note of the next chunk (which is on the beat) in order to practice connecting the chunk I’m practicing to the one immediately after it in order to make the transition between them smooth even before trying to connect two complete chunks.