How do I open a custom quest in Zelda.exe?

File/Open..

No, that's in Zquest.
In ZC, register your name, then press the button set to A (alt by default), then press it again. Click browse, find your quest, double click it, and press OK. Then press start as usual.

Enemy and item editors are being worked on. NPCs were scrapped a long time ago because they were too buggy using the current system. I expect they'll make a comeback when the enemy editor is implemented.

Took over the hijacked thread.

Enjoy!