This gives you your first shiny frame at frame 6314.
Download a program called eontimer and put this number in under the 3rd gen tab. It will convert it to a time. I can't remember the exact time delay that rayquaza had, but I *think* it was negative which I remember being really weird.
Anyway, if you download RNG Reporter, use these parameters:
Method: Method 1
Max results: 600
Starting frame: 6000 (this and the above can be changed, but this just gives about 5s around your shiny frame. If you are further off than this then decrease starting frame and increase max results)
ID: 43216, SID: 63941
Basically you want to SR start the game when you start the timer on eontimer and when it hits 0 hit A as close as possible. Catch rayquaza with a masterball (I hope you have one!) and then check it's IV's (you may need 1 or 2 rare candys to help). Once you have found out it's IV's, look around the shiny frame (6314 in the RNG reporter results) for the frame you hit. find the difference andmodify the frame you are trying to hit in eontimer byt his amount. Ie. if you are 10 frames early, add 10 frames to the eontimer number and go for that. Once you are hitting frames around the shiny one you won't need to keep checking the IV's and you can just keep SR-ing and pressing A at the specified time until your shiny rayquaza appears