One of the common problems one will possibly run into is the lack of Coins, because the Remake was redesigned so that anything you got out of the Pots do not come back if you reload your game.
When possible, the best way to make money is to summon a coin fairy (miracle.exe+capstar.exe [You don't need this rom combination, it just increases the chances of getting the right fairy]) and take it to Chamber of Extinction (E-4). Break the 4 bricks at the top-right of the room, grab the coins, exit to the right and repeat. You should be able to make around 500-700 (1000 with the bracers and axe) Coins in one fairy cycle. If you don't want to wait for the fairy to re-spawn, a good strategy is to exit to the room below and save, quit, and re-load the file. Do be careful, since the bricks can crush you if they fall on you, so jump first before striking.
Teleport to the Spring in the Sky grail point and make your way to D-5. Activate the fairy point, and if you get a star pattern that does not belong to the money fairy, go to C-5 before the star pattern has completed and try again until you get the right pattern. After that, warp back to the Surface, break the pot and go one screen to the right and dispatch the bird and pot there, then warp back to the Surface again. This takes advantage of the fact that the fairy timer is only ticking down when you're actually moving around, so by warping, you save yourself a decent amount of time. Depending on how lucky you get with coin denominations, this can get you anywhere from 100-200 coins per fairy. Having the item that lets you break pots in one hit works well with this method.
Similar to 'Method 2', teleport to Spring in the Sky and make your way to the fairy point. This area is good for summoning an item fairy before you obtain the (miracle.exe+capstar.exe) combination. Once you have the fairy, teleport to the Surface, drop down, and strike the pot at the entrance. Immediately go into your grail menu, and warp to the Gate of Guidance. Once there, walk to the right, dispatch the skeleton, and break the pot. Once the pot is broken, warp back to the Surface, rinse and repeat. This method involves roughly the same amount of walking as method 2, but for nearly 250-350 coins per run without perfume or the bracelet, with extra EXP or weights coming from the skeleton.