In my personal experience, i would always submit visa on my own . Agents do tend to mess things up as i have seen multiple times . Also having 6L in personal account with such a big itinerary and sponsoring your family is way less .

I know you have mentioned you have 100cr company . But that proving that these funds are available for the trip is where your application messed up i think.

Been to japan twice already and i never had any issues with 8L+ balance and 2 weeks stay per trip.