If I recall correctly after-tax and before tax money in 401ks come out proportionally. If I recall you take some money out then you'll get some of both (before and after tax money) and will pay taxes proportionally. I believe though that there is a way (a loophole) around this using a Roth IRA conversion for the after tax money. I suggest you speak to the people who hold your IRA (Vanguard ?)
If you throttle back the wife's payments into her 401K you lose both the income deduction on the payments and any company match. Without the company match reducing her contributions is kind-of equivalent to taking money out of your 401k (ignoring penalties).
Look into 72-t withdrawals from IRAs. That is one way to take (some) money out of an IRA without penalty (income taxes still due). here's a link to Fidelity's calculator