1. Yes, you must file nonresident tax return. The U.S. India tax treaty allows you standard deduction of $5,350 (same as for the residents). Read
Your U.S. Tax Return: U.S. Tax Treaties for Students and Apprentices
2. Your income is not subject to Social Security and Medicare taxes. If employer deducted these taxes, then send them email for the return of the taxes. Read about filing Form 843:
Your U.S. Tax Return: Social Security and Medicare (FICA) Taxes for Non-resident Exempt Individual
3. You will report 1099-Misc income on schedule C-EZ. For you it is not subject to SE taxes. How you will treat the 1099-Misc income, read:
Your U.S. Tax Return: W2 vs 1099-Misc: Employee vs Independent Contractor.
4. Now you will file amended tax return Form 1040X and a properly done nonresident tax return. May be IRS will not access any penalty if you file nonresident tax return on your own.
You can use the services of AtlantaTaxExpert (taxexpert@visataxes.com). He is one of the most experienced person to do non-resident tax return.