CiviEvent Confirmation Email Displaying Profiles Not Used In Event
Eric,
Disabling those fields should remove them from the confirmation email. If you can't disable them (maybe they are from another active event), you can edit the Event Registration Confirmation and Receipt message and target the Event using $event.id (as in {if $event.id != "40"}do such and such{/if} ).
Administer > CiviMail > Message Templates - System Workflow Messages
Good luck!