Just got this tonight, and I found that the best place to accumulate the rest of your coins needed after the two main playthroughs is on the Sand Level with the moonstones (level 10). After you fall down into the pit, you're going to want to "Panda Roll/Stumble" over and over and over again until you get the coins necessary to pay off what remains in the upgrade section. This took me little over 30 minutes to get the rest of my coins, and I had only beaten the game once on Dragon Warrior. Good luck!!
Also if you're up for putting in a cheat code to make this go faster, in the main menu, go under the "cheats" section and enter this: Down- Right-Left-Up-Down (this is for Infinite Chi so you can roll until you receive the necessary coin amount).