Thanks Jeff! I plan to rework my squat immediately following this meet. Based on all the great feedback here I am planning to utilize tempo and pause squats to force myself into the correct bar path.
I will keep this board updated on my progress.
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I have recently struggled with the same problem (best squat 5x410 at 200 bw).
What I have noticed is that as I get tired I tend to rush the bounce from the bottom. What I mean is that my wish to get the rep done exceeds my willpower to keep the hips driving the bar, and then the hips shoot up slightly, taking the strain off momentarily. This causes - to varying degrees - back angle becoming too horizontal, knees caving in and balance going first to the heel, then forward as counter measure.
A que I have been really consentrating on with great success is to drive my hips up WITH the bounce. This is crucial when getting to the end of the set. Instead of letting my hips loosely bounce from the bottom, causing them to go back, I conscisously have to slow down and really guide the bounce confidently. This feels awful by the end of the set, because the wish to not be under the bar is huge, but this fixes the back angle and knee caving issues for me.
tl;dr - Slow down your ascent, guide the bounce, don't let the bounce control you, keep your hips "under the bar" and don't be afraid to spend some time coming properly out of the hole, rather than just quickly.
I hope I am making sense, this is something I've just recently started figuring out.