Why would you file separate and more taxes. Remember if one spouse is claiming itemize deduction then the other spouse can't claim standard deduction. Plus the tax bracket changes in MFS as well. Claiming 40K deduction in 75k income will trigger AMT as well. I don't know what kind of job you do or travel you are referring too but claiming mileage in W2 income is a red flag. Normally employer reimburses all those mileage and cost of fuels.

I would suggest you file MFJ. And don't blame practitioner for your interest and penalties. You prolly didn't do your due diligence during the year.