OPT is considered F-1 too.

You can use 1040 since you are a resident for tax purposes. Because you are a student (including OPT), the 5000 treaty and fellowship exemptions both still apply.

I don't think you can get back your SS and medicare tax once you paid them. You should tell your payroll that you are not subject to those taxes because you are still on student visa and hopefully they will stop taking those amounts from your pay check.