Unfortunally, the only way to resolve your issue would be to take it to court. If he's not voluntarily giving you the money based on your agreement, then there's no other option.
However, it sounds like you have been getting the better side of the deal anyways. Basically, if you are making $25,000 more than him, and custody is 50/50, then you would owe child support. In order for your child to benifit from the income that both parents make in an income share model, then you would be entitled to pay him money. Not only would you have to pay him, but he would no longer be entitled to pay half. But instead, only a % based on yours/his total income. You may be better off eating the $3,000 as it appears you'd by much more than that in the long run. However, most people in this group would be quick to state - your getting out of paying child support that your child is entitled to - so your only hurting your child by going around the system.
Just for fun, I ran a senerio in the Tennessee Child Support worksheet, which may or may not be similar to Kansas's system, but if you made $65,000 and he made $40,000, and there were no child care expenses involved, then you would have to pay him $260 /month in child support.