Firstly, if you haven't had a response from John within a day to say he has it, there's a good chance it's been spammed (he has a pretty aggressive filter.) Certainly, he let me know when he received mine, recently, and gave me a good idea of turnaround time.
And then, I suppose, the age old question springs to mind - have you had it read by others? At least other writers, ones that you admire, and not just friends and family? I know it's a cliche, but I definitely sent mine out too soon the first time, and burned a lot of bridges with agents who I'm not able to query again.
Finally, does your query reflect the structure of the novel? Regardless of whether the first 3 chapters are different from the rest, they're the three you need to pull people in with, and if you're not sure they're doing that job - which it kind of sounds like you mightn't be - then they might need revised? It's just most agents will need to be hooked before chapter four - they really need to be at least interested in the first 1000 words (I'm being generous, btw) to read on.
Just some thoughts. Otherwise, John takes one of the largest samples of work. Most ask for either three chapters, ten pages, five pages, or just the query. Some don't read past the query if it doesn't hook. Depressing, isn't it? I'm turning into a right old Eeyore.
Oh, yeah, hi; welcome.