I need to get EIN to set up 401(k). Will I be able to file under new EIN and also get credit for my quarterly taxes I paid under SSN this year?

Quarterly taxes are always paid under your  SS#  and are entered on the federal return.  It has nothing to do with any business return or an EIN.   The EIN is added to the Sch C ... it doesn't replace your SS#.

https://www.irs.gov/businesses/small-businesses-self-employed/apply-for-an-employer-identification-number-ein-online