Thank you for your responses, Aoife and Cloud9Fitness. I had figured it might be a posterior chain issue, and had begun to add some hamstring isolation work along with my leg workouts.
For now I will stop lifting on the Leg day of the Hypertrophy II program and instead do the exercises you guys suggested three to four times a week. Hopefully that does enough for me to be able to get back to painless squatting and lunging.
I will report back on the results.
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