If she's otherwise healthy, but just under weight, you will both benefit in the long run from establishing a regular feeding pattern right now when she's actively feeding.
Do you have any idea how old this BP is or what she currently weighs? Are you sure two rat pups are enough for her at her current size. A rule of thumb is to feed a prey item that's 10 - 15% of the snake's weight. She might be cruising because she need a small or med rats instead of the rat pups. Having a scale and the ability to weigh her will be essential in determining her food size.
Personally I thinks it's better to feed the correct size prey item once a week, than to feed smaller items more regularly, but that's just my opinion developed out of my own exsperience. Other keeps have had great sucess with more regular feeding. Either way, I think it's important to establish a regular schedule for when you offer.
About the wobble. Some Spiders do it when they cruise around, some do it when they strike, some do it for no reason at all. It's a well documented condition and varies from snake to snake.
As for the small head. it's a Ball Python thing...they have skinny necks too. Part of the charm.