Just two words: Keep updated. This means keeping track of the latest version of Zelda Classic. I have played a couple games that had major bugs in them because they were created for older versions (I currently use version 2.10). If it makes no sense to start the designs of an engine designed for a Model T when more fuel-efficient cars are available, then it makes no sense to begin from scratch using ZeldaQuest 1.00 when 2.10 is available. Use the most recent version when you start.
Of course, I understand that quest building takes a long time, and during that long time, or even afterwards, a new version might come out. If case this happens, indicate which version you used to construct your quest. If a new version of Zelda Classic comes out after your quest is made, test your quest, or have your quest tested, using the latest version to check for major bugs. If any exist, try to update your quest (if you can do so without a lot of trouble).