i woudln't worry about it-
the only school that 'harshly' pre-secondary screens is ucsf - some people that got into many of the top schools were rejected pre-secondary there. otherwise it's not something to be too concerned about considering that most don't screen at all.
also don't worry about the publication thing - only two or three person in my class had publications [none in big name journals to my knowledge] and among us we were accepted to all the top schools in the country. again - its about presentation and a compelling reason to do an mdphd corroborated by appropriate experiences.