Okay well I fixed your mod.
Download Mountain of Light Fixed
This took a lot of hex editing on the executable to get it right. Now, when I first saw the exe, it just had the default icon and not the Doukutsu icon, which led me to think "Oh great..." because that means the resource section is definitely messed up.
I wrote a Mint program to analyze the mapdata and basically gave up before realizing that I could probably copy the working mapdata from the original Cave Story program.
Now, this may be fixed, but I think you should try to rename all your maps to the original names. I always suggest not changing the filenames of the maps. Once you do this, your mod should be back to normal.
So that's that. The mod does start up correctly and you can play it. Tell me what you think.
Next time, please don't mix Sue's Workshop and Booster's Lab.
Also remember to make lots and lots of backups.