1. If I take the girl to registrar office tomorrow, what will be the procedure?
You can marry her elsewhere in the presence of some witnesses and can apply for registration of marriage under special marriage act before the marriage registrar.
The witnesses who were present for the marriage can be witnesses to the marriage registration process too.
The formalities to be observed i.e., the documents to be carried while getting the marriage registered can be enquired from the local registrar's office.
2. If we apply for marriage under special marriage act (I saw the procedure as waiting period for a month) is it legal to be together during these waiting period?
You may have to wait for 30 days period if you apply for registration of marriage before solemnisation of marriage. You need not stay together during this waiting period.
3. If the girl passes on affidavit to the local police station stating that she is marrying on her own will and if her father goes to police what will the police do?
The police cannot do anything on the complaint by her father if she gives a clear statement stating that she is major by age and she has full rights to choose her life partner.
4. Can we marry at any church and get a certificate instead and do the registration later. Is it legal?
Yes you can do that. Solemnization of marriage is very important for getting the marriage registered.
5. Will the police take action against us if we marry?
The police cannot interfere in your marriage if both are of marriageable age.