Unique Overworld Boss (a la DoomGaze)/Creating New Area Question

(I just realized that I'd posted this originally in a TUTORIAL section. Yikes. The original I just deleted, and I'm now posting it here, where it is appropriate.)

Okay, I'm just starting to get into hex editing, ASM programming, and event editing, so I'm well aware that any answers I receive re: this question may be above my level of skill/knowledge. But I'm curious anyway, and it's better to ask now than to forget later.

As everybody knows, DoomGaze is a unique boss fought on the overworld map in the World of Ruin, and it runs (maintaining its damaged HP) if you don't kill it fast enough.

What I'm looking to do is to create a random boss event (using a completely scripted CzarDragon as the boss) that will be fought in ONE location (I'm currently thinking of using the WOR "Dragon Forest" (wherein are fought the Tyranosaurs and the Brachosaurs).

Quite frankly, I have no idea of how to go about this. I want the boss to be EXTREMELY rare (say, a 1/256 chance of encountering), to maintain an encounter zone within the boundaries of the aforementioned forest, and to maintain its HP a la DoomGaze should the party run, clasping their scorched behinds as they flee in terror (I plan on making the boss flee-able, of course, to facilitate this). How should I go about accomplishing this? I'm not asking for a step-by-step list to follow (though it would be nice, admittedly), but information that can get me looking in the right area and thinking in the right frame of mind.

On a side note, I'm also looking to create a new area on the Overworld of the WOR (where I plan on expanding those two single islands North of Thamasa) into a new area, wherein I plan to have a new dungeon. However, the editors that I have that ought to allow me to do this encounter problems: FF6LE will not allow any editing to the WOR world map for some strange reason, and the Final Fantasy 3 Map Editor 1.00 gives me the "Layer 1 is X bytes larger than the original map. Saving this map to the oringal[sic] memory location will undoubtably[sic] mess something up. Continue?" error.

Suffice to say, I DO NOT WANT to 'mess something up'. Is there any known way (preferably a patch of some variety)that will function with the FF3usME patches (and preferably LIKE said patches, ie, 'moving' data around while still retaining full functionality...and maybe expanding the rom to 48Mbits while we're at it) and NOT completely bugger it up?

This is related to my first question in that I primarily want to create my own version of FF6A's "Dragon's Den" for the SNES FFVI. I've already done things like patching the evade bug, restoring original graphics, and I'm practicing for the creation of my own translation, but I would like a hint or twelve on the creation of a unique area.

Thanks for all your help in advance.