why do you want do get so much deeper? you are training for powerlifting or not? slightly below parallel should be enough then.
I remember reading, I think from Mike Boyle years ago that you should "learn to squat deep before squatting heavy" - phrased how I remember it, may not be exact.
Not much has turned out to be more true. Not everyone will be able to squat to the same depth but you should be able to move safely and efficiently through the ROM your body will allow.
A quick screen I use to determine this is here - don't know who it is I just searched on youtube.http://www.youtube.com/watch?v=8rc2E_jkuM8
This is a squat on all 4's. The significance is, it takes away the need to stabilise your body. I like to get an arched back and have clients rock back until they just start to lose their arch. Just before this point is where I want them to be able to squat to before we start squatting heavy. Most men over 30 won't get any where near this ROM when standing. This is a problem! You have to ask what changes when you stand up? The short answer is, you have a stability problem. Your brain now has to worry about NOT falling over so if something in the chain isn't doing what it's supposed to, the brain will shut things down or, "put on the brakes" - in other words, shorten your ROM or achieve the ROM with undesired compensation (like lumbar flexion).
In Kens case, if he can kneeling-rock-back way deeper than he can back squat, then he needs to find and work on a stability fix - most often some kind of anterior core issue (evident if you can front/goblet squat deeper than back squat). If it's the same, then he has a flexibility issue and needs a boatload of foam rolling and stretching along side some stability work - you should always use both (stability and flexibility drills), but your specific problems indicate what you need more of.
Going back to the quote I started with, I have learned that if we make you squat high and heavy when you can't squat deep and efficiently, you will be ok until you get to a certain -and individual- level of strength/fitness which will take you beyond your threshold. This is when aches and pains kick in and, if nothing changes and you keep pushing, injury.
Now, I'll still use a high squat to teach good squat form. Quite often use Box Squats above parallel to teach hip hinging in a squat. We'll use load, yes, but won't be pushing for strength. It'll most often be in some kind of circuit or superset, the emphasise is not on adding more load.
The bottom line is, if you struggle to get into the bottom position of a squat with good form, you will not realise your true strength potential. It should be effortless without load. If it's not, then this should be addressed, and not only will aches and pains magically disappear, you'll be stronger, too, because that effort needed to get into position can be used to actually push weight.