In the manual it states that if you are more than 50 lbs. overweight you do not need to begin the shuffle until you have lost the excess weight. Do you still advise this?

Yes because your heart rate will typically already be in it's target fat burning zone just by walking. Imagine walking around carrying bowling balls, that would be intense. Essentially that is what it happening by walking around carrying excess weight. Pay attention to your target heart rate and increase the shuffle as you decrease your fat.