That's always been the problem with CA's games. There's really steep diminishing returns when it comes to economic buildings. The early buildings are just way better than the later ones. The "upgrades" are more expensive yet add less.

I've had some money problems early in the game. Mostly it's the Spanish and Pirates who I'm at war with. The other is that UP starts trading with both Maratha and Mughal and they keep blocking each other's port.