If I can't find proper shoes for squatting and dead lifting, I might have to skip the squat/dead program for now.
There is one more option - http://www.veganwares.com
, they might be able to make you a shoe that's suitable for lifting, and they can make ANY size/width shoe you could ever need. Might want to check with them on that!
Then to make things worse, my doctor tells me I will end up with back problems and most likely other issues involving the CNS and peripheral nerves if I squat with heavy weight on my back compressing my spine. Not that I agree but ofcourse it is in the back of my head.
Is there a pre-existing condition that your doctor is stating this for, or is it simply the standard "physician's ignorance of exercise" that is the culprit? If you don't have a pre-existing condition, then their opinion is completely invalid. Then again, physicians are typically the first people to say to stop exercising completely when you get hurt, perpetuating the cycle of being physically weakened with little to no chance of strengthening the injured areas again, making one worse off over time. Sad, but that's how too many physicians think is the best approach, simply because they have a lack of training in anything related to exercise science and rehabilitation. If you have questions beyond your doctor, seek out a qualified physical therapist who deals in sports medicine - I'm sure you'll get a very, very different opinion from someone who has studied exercise and rehabilitation in-depth vs. a general practitioner who spends more time looking at blood pressure readings and prescribing Lipitor than they do furthering their knowledge on fixing real physical problems via strength training.
Then I still have the fear of overlapping muscle groups. Deads and squats the same day is a problem for me because my back is still sore from back day by the time I hit deads.
Then, it is easy - put a few days between your squats and deadlifts!
I never do them with less than 2 days between to allow for proper lower back recovery, so it's not just you, there are more of us who don't feel that both lifts are best to be done on the same day. It may mean that some training programs need modification or just won't work out right doing it this way, but you have to do what's best for YOU vs. sticking to a protocol because so-and-so says to squat and DL on the same day.
I want to do the most effective exercises for quads which I believe are squats and the most effective for hams which I believe are stiff legged deads.
One thing to note, you will be using your hams to some degree on squats, depending on your stance and technique it could be a little or a lot. The more you push through your heels, the more recruitment you're going to feel vs. the not-so-great off-the-toes style that many people fall into. When I squat, I feel about 75% quads and the rest in the rear, but that of course varies from person to person. Stiff legged deads are great, but also consider Romanian deadlifts, as well as single-legged SLDLs and RDLs which to me REALLY hammer the hips, glutes and hams more than barbell style does whenever I try them. If you have access to a glute/ham machine, that's another option as well. And, of course, if you're lucky enough to have access to a reverse hyper machine, you'll have everything you need for a strong lower body right there.
Hope that things go well, don't give up hope on those squats and deadlifts just yet!