Major foot mistake

So just a brief history .. last bike tour from San Diego to Phx I found out Clip pedals was not a safe choice .. trying to start from a stop .. on a incline with loaded panniers .. in heavy traffic .. narrow shoulder ... dangerous at best .. so I went to a Flat pedal with screw in pins .. great choice .. foot does not slip off pedals .. quick orientations to get back onto the pedals keeping the bike moving forward .. Con was .. the pins where chewing up the soles of my cycling shoes .. Hmm .. what to do .. so I got this idea of trying Vans ... the soles seemed to be impervious to damage from the pins .. so much so that I ended up buying two pairs trading them off every other day while training on my indoor trainer .. have been using them for the past 2 yrs or so .. 6 times a week ... 1 to 1½ hours per day .. finally I developed sever pain in both the balls of my feet and at first it was thought I had Morton's Neuromas .. shots of cortisone had no effect on the pain ... MRI later showed no Neuromas but Lesions developed in the balls of my feet ... at this point treatment seems to be orthotics .. no cycling .. and maybe a looong term off the bike ...so they Hopefully heal .... I only post this for general info