Correcting Poor squat form

I have searched the Internet and can't seem to find an answer to my question and hoping you experienced lifters can help...

I've been lifting for almost a year, switching between sl5x5 and nrolw, progressing well until my ankles/front calf starting hurting when squatting as the weight got heavier. Referred back to proper form videos and searched forums for people with similar problems and worked out I was leaning on my toes, probably due to a flexibility issue. Felt downhearted for a while as if all the work was for nothing as it was all with inproper from. So started SL again from the begining, squatting with an empty bar. The problem is I can't squat properly, if I don't lean on my toes I don't get more than half way to parallel, if I try and distribute my weight evenly across my feet I feel like I'm going to fall back as soon as i start going down.
I have been doing wide leg squats which I find comfortable and can get lower than parallel but I don't know if there is any point doing wide leg. Is there anyway to correct my previously poor squat form or how to work on getting it right?