HUGE UPDATE: My biggest issue with hacking the stages has now officially vanished. See the pic below:
This is a screenshot of the lower left quadrant of vram in a room in the chapel... as you can see every enemy in the stage has been loaded into vram, and even object type sprites. Those of you who know a little bit about programming, probably already know what I am about to say, but for those of you who don't it means that I have after over TWO YEARS found a way to control what is loaded into vram and where! This eliminates the biggest problem I had: not being able to put enemies wherever I wanted to put them (in the past they would come out scrambled or invisible due to this). The only limitation is that the enemy MUST APPEAR in the current stage (only the enemies that appear in the stage have their AI and gxf stored in the stage file, thus making them loadable)!
Many thanks go to Nyxoale for this! He spent about 4 hours on IM with me showing me how it could be done, and then this info combined with my findings allowed me to figure the rest out. Thanks also go out to Gemini, who provided me with some VERY useful info years ago that helped me to figure out how to change some necessary values as well!
Also.... here is a quick animation of the new gates that will be used in my rooms to close them off when you have to kill all the enemies to proceed forward (it has been slowed down so it is easier to see; the actual one is MUCH faster):
It is a 9 tile animation (I couldn't use sprites due to limitations), but even though it is using tiles as you can see it is not choppy looking at all. These are the exact gates from curse of darkness, rendered into beautiful 2d.
EDIT: smoothed out the above gate to make it blend better. Here is a screenshot: