Man congrats on the fat loss. Keep doing what you are doing. However if you want to experiment with the peri-workout and post-workout nutrition there is an author here by the name of Shugart that wrote a very thorough article on this same issue and the results are very promising.
Now with respect to the issue of your bulging disks I also have 3 (S1,L4,T7) and the first thing you should be doing is getting your lower back stronger than any other region in your body. In fact you should look into getting your whole posterior chain stronger than any other parts because they support your spine and it will carry over to everyday tasks.
There are many ways to do this, but I recommend you do a google search for "hip-belt squats". Ironmind carries the one I used at that time. It's a special belt you strap on your waist and can then attach a barbell or cables or pin to it so you can squat and the weight is carried by your hips and not your spine. The position is similar to the squat and will help with getting the groove for using your bodyweight plus whatever amount you strap yourself to.
Aside from that if you can get a hold of 2 other pieces of equipment you will be set. One is called "reverse hyper" and the other is called "glute-ham raise". Do a search here and there are tons of videos with examples. They will build your back, glutes and legs withougt compromising your disks.
At the same time start practicing the movement with an empty bar. Not to add weight but for the movement pattern. See where it hurts and how far down you can go safely. Go down until you feel no "hurting" pain but still feeling the strain of the muscles. Work on your flexibility if this range is higher than the hips being lower than the knees. Do flexibility work 3 or 4 times per week after warming up or doing your cardio.
I don't know how much time it will take you, since all bodies are different. But, you can squat and deadlift safely if you strengthen the muscles, since it's obvious that they are atrophied from lack of use.