Hi, seeing you around sooner than I thought:)
I had a look at your hack, Hidden Ties (I've seen it like today, I didn't know twas you who'd done it, even though I posted there a couple months ago, haha). Anyways, I know you have a subplot lined up, but I may be able to help with your map connection problem? It happened to me in Emerald (on my last hack that had the scripting bug), when I'd exit one map into another, the game would freeze. If I tried to warp there, the screen would go black, and the game would freeze. Eventually, all I had to do was open the Connections editor, and change a value. Trouble is, I'm not at home, so I can't look at A-Map, thus I can't tell you for sure. I think it was whichever box has four digits in it, the non-glitched map had "0000" while the glitched map had "0080". I just changed that 8 to another 0, and it worked. Sorry if you tried that already, and for being a tad vague:) Good luck with your hack, though, it looks very promising!