Use one of the Jobs near the bottom of the list (Near Ultima Demon, etc.), and use the M.Graphic and M.Palette options to set the Job's sprite and portrait to that of the Yellow Chocobo. As for setting up his WLDFACE info, I believe it's Glain who has a Spreadsheet that lets you re-point unused entries, so you can grab an unused entry (such as the Ultima Demon), then ferry it over to Boco.
This combined with making sure Boco is set to Monster Gender (very important!) should fix your problem.