Okay, there's your first problem. You are moving too fast. I'm not familiar with Meg's pads so I apologize for asking where it falls in the aggresiveness scale. Is it a cutting or polishing pad? Since you are doing all the cutting needed with your rotary and SSR3, I would use a good polishing pad with SSR2. Spraying your pad in the beginning is fine and will aid in the priming process. You are doing good by only doing a 2x2 area at a time but you need to slow it down with the movement. Slower is always better with a PC, and always use overlapping passes. The speed should be around 4.5 with just a little bit of pressure applied. Moving at a snails pace, you should slowly decrease the amount of pressure until only the weight of the machine is left and increase the speed to 5. I like to stay on speed 5 because this gives you a longer period of time to work the product in before it dries (hazes) on you. Once it dries to a haze (or starts to dust, depending on the product), stop and remove the excess, inspect your work, and move on. If you still see imperfetions, do the area again. Once you are completely happy with the finish, THEN move to SSR1 with a finish polishing pad using the same process as described above. Just remember to move slowly, patience is the key, the rest will come in time and experience.
I recommend two things for you to do, watch the Meguiar's videos and read the Autopia Guide To Detailing. Both will help you a great deal.