Unfortunately, Comet2 is limited by the statistical parameters of the spell: damage per comet is only 1 7/8 times base, while KotR is (to compare) 5x base. Moreover, while increasing the number of hits, Quadra Magic will also reduce the damage of the hits. Further still, as pertains to the Ruby Weapon fight, KotR is far superior by virtue of its defense-ignoring qualities. This is why it still hits for normal damage against Ruby, while most attacks drop to nearly nothing.

One way to boost this combination beyond the damage you've seen so far would be to use it in conjunction with All Lucky 7s. This is limited by the fact that only Emerald and Ruby can withstand the initial sequence of damage, but your combination combined with 7777 HP would result in 32 hits of 7777 damage against those two foes.