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No, they are not removed when you select standard deduction on the federal return.  The medical expenses are ignored on your federal return if you are using the standard deduction.  But they are still available to use on your state return if your state allows using a different deduction.  Some states allow you to change, some don't.   The expenses are entered on your federal return and transferred to your state return(s).   If your medical deduction was not included on your NJ, you can amend to add the deduction.     NJ doesn't have a standard deduction or itemize deductions.   New Jersey law provides several gross income tax deductions that can be taken on the New Jersey Income Tax return. New Jersey does not allow federal deductions, such as mortgage interest, employee business expenses, and IRA and Keogh Plan contributions.      On your NJ return, you can deduct from your gross income certain medical expenses that you paid during the year for yourself, your spouse or domestic partner, and your dependents. However, you cannot deduct expenses for which you were reimbursed. Only expenses that exceed 2% of your income can be deducted.   See NJ Exemptions & Deductions

The calculated penalty may have had to do with the timeliness of your estimated payments?  Did you make some of them late or make all of them in the last part of the year?  Or pay a bunch with an extension?   @gomes_f 

If you set up direct debits, I would not expect vouchers to print. I would watch and make sure your payments post to your accounts.   List of Department of Revenue by state  List of state DOR's  Call IRS e-file Payment Services 24/7 at 1-888-353-4537 to inquire about your payment.    

Yes, as long as the organization treats the individual as an employee and the housing allowance is officially designated as such before payment is made.   See IRS Tax Topic 417 for what is considered and employee and the rules for the housing allowance.   @Noah18 

If my memory serves me correctly When completing the federal return turbo tax system checks to see if standard deduction is a better option, once a person chose standard deduction did that kick out the medical deduction information ??