Specifically can we take $3,000 out of flex spending, pre-tax, and then file a form 2441 for the remaining $2,000 as taxable income?
Actually that is exactly what you need to do ... however you can take the entire $5K from the FSA account to pay for the day care expenses so you don't forfeit that money ... that is still allowed. The form 2441 will simply put the excess back into income by adding it to the wages line.
