Good to hear you are improving your squat technique.
Pro Episode #5 – Knee Stability and Laxity
Pro Episode #20 – Dealing With That Horror Show Bump On Your Knee/Osgood Schlatter
Spine first as the spine is the carriage or chasse for the primary engines of the shoulder and hip.
Disorganized at the pelvis hip function is decreased.
Changing the position is the way to improve the function.
Carl Paoli, GWOD, has a great video on blocking movements for quality squats.
Blocking Movement for Quality Squats

Jorge,
  It’s good to see you know what your limitations are with mobility and technique.  While you are working on fixing technical issues I would look into doing the couch stretch and smashing the quads.  Simply put, the anterior hip all connects into the patella/quad tendon which is anchored on the tibial tuberosity (Osgood bump).  It you get the anterior hip to open up it should relieve the tension on the bump some.

So in summary, continue focusing on technique and overall mobility, but put some extra work into the anterior hip in the form of the couch stretch (and other anterior hip stretches) and smashing.  My favorite for smashing is barbell smashing the quad at night while winding down in front of the tv.  Also, look at your squat technique and make sure you are breaking at the hips first.  This will help keep the patella tendon from being tacked down first and taking the brunt of load in the squat.  Also, keep the shins as vertical as possible.  This will help keep tension off the knee and into the hips.

If you have anymore questions please ask.  Good luck.

Jorge,
   Yes opening the anterior hip can help with butt wink.  You can determine if butt wink is a mobility issue or stability issue by kneeling on all fours on the floor.  Make your knees as wide as you normally squat and rock back until your butt sits on your heels.  Either film this or have someone with a good eye watch your hips.  Start by doing it with no ab bracing at all.  You should see your hips butt wink.  Next, brace like you would with a squat and go again. IF your hips stay solid with bracing it is not a mobility issue.  IF they still wink, you are most likely looking at mobility.  You can also play with this to see what your ideal squat width is.  This is a Dr Stuart McGill strategy (I think. He uses it to determine stance width).  I’m not sure if you can find a video of this online.

   Hope this helps.

Honestly, I think I stated this backwards the first time. (It’s been fixed for anyone else looking at this post)

If your hips stay solid with bracing on, it IS NOT a mobility issue.  You can achieve proper depth with a stable midline and have all the ROM required to do so. 

If your hips tuck under with bracing, it IS a mobility issue.  When you achieve proper depth you go into posterior pelvic tilt (butt wink) and this is what is shutting your abs down, in my opinion. 

Try doing the same movements as a body weight squat and see if you get the same results.

Overall, you first need to be organized and extremely stable under load.  The WHOLE time too.  If you are losing stability in the bottom, make sure you are really screwing your feet into the ground and maintaining that initial tension.  Secondly, you need to have the ROM to perform deep squats.  You have already pointed out what needs the work; anterior hip, ankles, and hips.  For now, I would squat higher, to a box or free, until you can fix the butt wink.  Then add a little more depth when you are sure you can maintain neutral.