Some options for holding the cotton balls and pj - not sure how well these will work or how they will price out in the quantities you need.

Altoids has smaller tins for their sugar free mints. These look like they would fit inside the standard Altoids tin. I think the chewing gum tins are even smaller.

A small (single dose) plastic pill case would probably work well also. I think you can find something similar in craft/dollar stores for organizing beads.

Here is a link with lots of images/ideas.

Going cheaper, maybe get some extra wide drinking straws from a local gas station/kwik mart (some around here have 1/4" and even 1/2" diameter straws) and figure out some way to seal the ends (tape, melting, glue). Going to the local Hardware store and picking up some cheap plastic tubing would probably work well also and be a bit sturdier in use.

Good luck on the kit.

- Eric