I've looked at the latest versions of this game and I can't really see any differences. So I'm just sticking with V1. How did I do this? I used Game Maker Editor which is a graphical version QuickBMS. Then I used Paint.net to fill in the transparencies. Finally MS Paint to copy/paste. I'm sure I missed a few. I was only going for stuff unique to this game and it's hard to see anything in that Kludge. The sprites aren't laid out in separate sheets in nice neat rows like they are in Rosenkreuzstilette.
This seems to be a thing with Game Maker. Another Metroid 2 remake was just like this.