Boss Battle Strategy
He will counterattack the entire party very often if he is hit by a character that is not close by. It is recommended to only attack with a character that is physically close to him (the battle screen will show "Too close, can't counterattack.").
Quick Kill Strategy
Have Crono and Frog use X-Strike on Yakra as often as possible. There is no need to heal, as Yakra will die within only a few uses of the tech. Lucca should not do anything unless healing if by chance Yakra somehow manages to seriously injure the party, which would only happen if Lucca helped provoke Yakra's counter-attack.