Massive amounts of trial and error (and dedication).
There is still a boss that has been around for like, 5 years now, Absolute Virtue, that hasn't been legitimately killed. People figured out a way to get him stuck on a rock and killed him, and Square immediately patched the exploit out. Then, people figured out you could zerg rush him with an alliance of dark knights with kraken clubs. Within a day Square quickly patched that out. After that everyone gave up, and now with all of the new content the items AV drops aren't even worth trying for anymore :lol
IIRC they didn't nerf Panda Ward at all, they only implemented the 2 hour limit to avoid having another group try for another 24 hours and generate even more bad publicity towards the game.
Edit: They did lower his HP to make him killable in a 2-hour timeframe, but they didn't make him any "easier".