I beat Emerald without using any secret material found using the chocobo's. I used just plain limit breaks and attacks.

I used Cloud, Tifa, and Cid (it does not matter what characters you use for they will be mainly curing anyway). I also had a master "green" material. This did not help me one bit. I suggest just getting Life2 attached with a mastered ALL and have Regan with a mastered ALL material. For everyone else, just put Double Cut material with 4x on Cloud and have everyone with the Couter Attack material on.

Right at the beggining of the battle I had their limit breaks all the way up (Omnislash is a must). Don't use them RIGHT away. Wait for him to attack first and have someone give them an X-Potion right away. Do this after every time someone attacks because he can attack twice as quickly as you can. You can use Regan, but it only really helps when he does the Stomp attack on all your allies, which is annoying. Your going to need to use megaelixers when Emeralds sholders come up. Just make sure you have 2 people curing and Cloud using his 4x Cut after every turn. Also the Counter Attacks will pretty much wipe the 4 crystals away soon.

Also note as someone said above that his "Aire Terra" move (or whatever it is called) will take 9999 if you have 9 material attached to on guy. Make sure that they only have at least 4 or less. This makes his attack mainly obsolete. Other then that, the Omnislash will probably wipe him away after a couple of times if you've gotten a bunch of 4x cuts in. YOU DO NOT NEED THE UNDERWATER MATERIAL. I killed him with 7:40 seconds left. The underwater material is not needed if you are strong enough.

Ruby Weapon...I'm still working on. =)