Running Gear: Deep shoe well

This is actually a question about children's running shoes.  My eight year old has a constant bruise over his right big toe (up on the knuckle connecting to the foot) due to his shoe.  At times, it is so bad that he limps a bit.  We have tried numerous brands of shoes over the years and cannot find anything to prevent it.  We took him to have x-rays about a year ago and were told everything was fine.  His doctor recommended a "deep welled" shoe.  We took him straight to an athletic shoe store and they analyzed his gait and the shape of his foot.  We ended up purchasing a pair of New Balance that were recommended by the salesman. The bruising improved, but did not completely go away.  We have tried the moleskin patches to prevent friction (thinking that may be the culprit), but they won't stay put.  If there is anyone out there who is knowledgeable about this type of issue, I would appreciate any advice on shoe brands, cushions, socks, etc.  The poor kid wants so badly to run with me sometimes, but knows his foot will suffer if he goes too far.  Plus, soccer season is starting and his kick is no good if he favors his poor toe. 

Thanks!!!