Congratulations on the extra income. The limit on 401k is 18,500 this year, but I assume you're funding to the max. You're likely ineligible for deductible Traditional IRAs, but could be funding Roth IRAs (doesn't help your current tax situation). However, with your student loan rate, I don't see an issue with prioritizing loan paydown over a Roth IRA.
For tax withholding, if you take two similar incomes and have them both withholding as MFJ+1, you are likely going to end up with an unpleasant tax bill. A decent solution is to have the higher income withholding filed as MFJ+1, and the lower income as Single.
You could also play around with tax software, or even just forms + tax tables, to predict your tax bill vs your current rates of withholding, and adjust your W-4s accordingly.