The second floor is pretty simple. Get on your Mach Bike, and ride down across the broken floor, left, and then go up, moving to the right and back up before you hit the rocks. It might take a few attempts, but this is the easy floor.
The 4th floor is much harder. It took me well over an hour of attempts to get past, and it's rather frustrating. What you need to is, ride the bike down from the door entrance, then turn left. This has to be done in the middle row - there are 3 squares in between the bottom section, the top part and bottom part is littered with rocks. Right near the end of this part, is a rock in the middle part.
At this point, you need to go straight up from the rock in the middle, before you hit it. At the top, there is a section like this:
0X0XX0X
Where the X's are broken floor parts. What you need to do is ride across so you stop in the middle section, with the two sections of broken floor next to each other. Don't go past them, or you'll have to go through all that again. What I recommend is saving just before that part, and then retrying if you fail. Do a soft reset (Start + Select + A + B) and retry from the saved point.
From here, just make your way up to Rayquaza. Hope you brought plenty of Ultra Balls! (BTW, he only took 2 Ultra Balls for me to catch, so maybe he's not all that bad).
