So If I remember correctly, there was some sort of event based system or patch that existed that let you rise above the original RM2k3 damage limit, I forgot if this even existed or not... But I know for a fact this is possible when configuring a CBS... But what about the original battle system?

I think you're quite possibly and almost definitely looking for the Goliath patch, you can find it on google.

Well I have the David patch installed, but that's just a smaller resolutionized version of the Goliath patch. So the contents are exactly the same. The max damage for a character is still only 9999... Hmm

Actually in most RPG's, if your able to go up to 9999 damage, 9 times out of 10, your dealing more damage than 9999, it's just the games coding that makes it only show 9999 damage. Same with RM2K3.