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@mduntoor has your name changed recently? (divorce, marriage, etc?)   otherwise, go back and re-key your SSN and your last name.  The first four letters of your last name and the SSN have to match EXACTLY to IRS database.    if still no luck, paper file. 

Yes. You can use mileage or actual expenses. All is explained here.  https://turbotax.intuit.com/tax-tips/self-employment-taxes/maximizing-tax-deductions-for-the-business-use-of-your-car/amp/L1rikLUJ7      

Can I take 179 depreciation towards my W2? In short, no.  The S-Corp files it's own physically separate tax return on IRS Form 1120-S. For the S-Corp, wages paid are a business expense. Any depreciable assets owned by the S-Corp are depreciated by the S-Corp and only on the 1120-S.  If you are a W-2 employee of the S-Corp (which is perfectly fine) you can't take any business expenses for the S-Corp on your personal 1040 tax return. The S-Corp is treated as it's own physically separate taxable entity. 

The FTB Notice should have listed what you have paid for that tax year.  Take a look and see if any of your payments are missing.   The next step is to make sure your missing payment has cleared your bank.  If it has cleared your bank, get hold of a copy of the cancelled check, if it was paid by check.  There should be a number stamped on the front of the check. Call the FTB using the phone number on the Notice you received from the FTB.  Alternatively, open a MyFTB account at www.ftb.ca.gov and look for the missing payment.   There may be various reasons for the payment to be misapplied.  Your SSN number could be wrong on the voucher, the payment could be mailed with a wrong voucher resulting the payment being applied to a different year, sometimes, when the payment is paid by the spouse using the spouse SSN, the payment could be credited to the spouse's FTB account, among others.   You may want to consider paying your taxes electronically in future.  They are much more accurate and safe.   In any event, here are things you can get from your MyFTB account MyFTB MyFTB gives individuals, ... online access to tax account information and online services. Features View account balance and tax year or account period details View estimated payments and credits before filing a return View payment history View a list and images of tax returns View a list and images of notices and correspondence View and update contact information View and protest proposed assessments and proposed adjustments to carryover amount View FTB hearing information and upload documents View a list of authorized representatives and manage who can access your account View a list of activities that occurred on your account, such as the last time you or your authorized representative accessed your account Calculate a balance due for a date in the future File a Power of Attorney (POA) File a nonresident withholding waiver request Chat with a customer service representative about confidential matters Send a secure message with attachments and specify if you are responding to a prior notice, correspondence, or online application Choose to receive an email when we send you a notice or correspondence Additional features Individuals View California wage and withholding information View FTB-issued liens, withholding orders, and Forms 1099 Respond to a proposed assessment to request a 30-day deferral to file a tax return Request a 30-day delay to pay certain types of bills Request an Individual Status Letter for the current tax year Access CalFile and Web Pay Request and manage payment plan Request innocent joint filer relief Submit an offer in compromise Respond to a Tax Return Missing Information notice (FTB 4306)