Well, it looks like you did everything right. I've been trying some things out throughout my free time today and it appears that were some oversights on my part when I made this program, as well as some things that I could have sworn I fixed but somehow must have broken some time later when I was adding features. The first thing I'll note is that your mod has capitalized "BMP" images, which the program doesn't recognize. So in order to have all your images recognized, you'd better change it to lowercase bmp or pbm in Cave Editor or Booster's Lab. I don't know why it's not detecting any of your modified .pxm or .pxe files, and I also don't know why it's not detecting the different map data and generating a modified stage.tbl accordingly. I'm almost positive I had this all working in an earlier release.
My sincere apologies for these issues, I think that a new release with these bugfixes will be in order. Unfortunately, I'm pretty busy with college course work, so I'm probably not going to be able to get a new release out until late May at earliest. Until then, what you can do is see how the stage.tbl file in CS+ is constructed, and use a hex editor to make your own stage.tbl in accordance with the map data of your mod. And then manually replace the .pxm and .pxe files that are modified in your mod. That last part is very straightforward.
Sorry again for these problems. If you really want to get this mod ported soon but don't want to go to those measures, then I can look through my earlier releases and find out which versions had the "Replace stage folder" and the replacing stage.tbl working, and refer you to that version to get your resources working.