When I put my sandwich together I make sure that the backing is quite taut (but not overstretched). Then I smooth the batting and pat down the top until it is also taut. I pin about hand-width apart. Have not had problems.
I believe that your SIDs are too far apart, but you can add lines inbetween. Odds are, your stitches were a little too tiny and the poor foot had trouble keeping up. I set my stitch length to 3 or 3.5 (Compared to 2 or 2.5 for piecing)
Good luck. You are way more patient than I would be. If my quilt wants to misbehave twice, it stays the way it is puckers and all.