I keep running into an issue with my custom tiles. The quality of the tiles are majorly reduced whenever ran through the conversion process of the program "LunaticPal",  Here's a link to the program: https://wombat.platymuus.com/lunaticpal/. I was hoping someone could give me some guidance and any tips on what I am doing wrong. I want to run my tiles through the program so I can use them for the game without ruining their quality, I feel like I must be doing something wrong. Please help soon as you can, this way I can know if I should give up making custom tiles or if I should keep going with what I started. Thank you!

The game runs on 256 colours, so if you use a colour that's not one of the 256 colours, it will look weird.

You could try loading one of the original tile sets and using an eyedropper-like tool to copy a colour you like.