Firstly, this should be in the training forum rather than the juicer forum.
Is the pain you're currently suffering from the recent squats just DOMS from the workout or have you aggravated your problem?
If it's an aggravation of your problem, have you been keeping up with the stretching? Did you keep the weight ultra-light for your first day back at an exercise after a long layoff?
That you can't do a full, deep squat with your feet together points to a serious inflexibity. Do you stretch out your hamstrings on a regular basis? Can you do a deep, hamstrings pressed hard against calves, squat with just bodyweight? Can you do it while holding onto something for support.
If your problem is just one of flexibility then I'd suggest keeping up with your stretching, especially your hamstrings, and doing bodyweight squats until they aren't a problem for you. Next move onto using just the bar, always going fully deep. Slowly add weight to the bar.
Due to a knee injury I had to go through this procedure and went through some time just adding 2.5Kg to the bar for 5 sets of 5 for four or five sessions per week. The weight soon mounts up until one day you realise that you're squatting sensible weights again.
Have you considered box-squats, front squats and good mornings?