After we are married, can he file for his green card, EAD Card, SSN etc. without any repercussions as to his expired visa?

Generally, a U.S. citizen may marry a foreign national who entered the U.S. lawfully and with inspection, such as with an F1 student visa, and then the couple can complete the adjustment of status application process for the foreign national spouse to become a Permanent Resident (to get a "Green Card"). This is true regardless of whether the foreign national spouse may have long overstayed his initial visa, and there would be no need to obtain any sort of letter asking for a pardon. If the foreign national entered with a J-1 exchange visitor visa, then it becomes necessary to examine whether that visa was subject to a "two-year home residency requirement." If subject to that requirement, then depending upon all of the circumstances, it may be possible to apply to have that requirement waived. In the adjustment of status application process, if the U.S. citizen spouse does not have sufficient documentable income to meet the published Poverty Guidelines for the applicable family size, then it would become necessary to have a "joint sponsor" for the application. Generally any U.S. citizen or Permanent Resident with sufficient documentable income and who is willing to assume the obligations specified on the Affidavit of Support may serve as a joint sponsor. Some immigration law firms, including mine, offer legal services on a "flat fee" basis so that a client will know the total expense from the very beginning, and a few immigration law firms, including mine, offer an initial consultation free of charge.