Once you understand how the economy and food work, money is easy. It is vastly different from M2's economy, which was pretty vague.
It's all about town wealth, and increasing your town wealth. Town wealth can gain one-time increases from things like improving resources, ports, and sake dens. Things like markets and roads add a small amount to town growth each turn, which can add up big by the end of the game. Having a surplus of food will also add to town growth.
And this food surplus is not at the individual town level; it is clan-wide. So if you have 4 towns, and 3 of the towns have +1 food each, but your third town at -1 food... then your clan has a total of +2 food. This means that ALL 4 of your towns will gain +2 to wealth each turn, even the town that has a food deficit. All that matters is your total food for your clan. Since town growth early-mid game significantly increases your late-game income, you want to try to increase town growth early and often.
What I generally do... (and it works pretty well) ...for growing economy:
Do not upgrade castles to a level higher than the farm in that region in the early-mid stages of the game. You don't want any towns to have a food deficit.
Get the research that allows level 3 farms as early as possible. This way, you can have level 3 castles, which will allow you to build what you need.
The 3 buildings you need to put in (almost) every town: market, sake den, religion building.
Do not ever upgrade the market beyond the first level, otherwise it will start to consume food. Maybe in the late game, you can upgrade a few.
Upgrade sake dens as far as possible, they give you happiness and money, win-win.
Religious buildings keep people happy, convert to your religion, and help with research speed, so you want lots of these as well. Since these don't give money tho, they have lower priority.
If you have to make a choice, I would generally upgrade in this order... Roads > Farm > Market > Resource > Port > Sake Den > Anything else. Roads first, because they help your army heal and move quicker, and they also add to town growth. Farms next, because they add to town growth to EVERY town you own, plus they give a sizable one-time increase to town wealth. If you can't afford a farm, but you CAN afford a sake den, don't wait a turn, just get the sake den.
Trade with as many clans as possible.
Make fleets to go capture the foreign trade spots.
Do this, and you can be making 10k per turn with less than 10 towns owned, fielding 2 full stacks of samurai, and 2 full stack navies.
If economy is that much of a problem, play as Otomo or Shimazu, since they are close to all the trade spots, you can grab them all early. Or be Chosokabe, who gets bonus income from farms.