Is it permissible to marry a girl who had an intimate relationship without losing her virginity, given her father's refusal to the marriage due to her nervousness and his demand for a large deferred dowry and an apartment in another location?

You are not obligated to marry the girl. The expiation for what you fell into with her is sincere repentance, which involves abandoning the sin, regretting having committed it, and resolving not to return to it, along with concealing it and not publicizing it, and increasing good deeds. If your repentance is sincere, then rejoice in Allah's forgiveness, and do not fear that your female relatives will fall into sin because of your transgression, for sincere repentance erases what came before it, and one who repents is like one who has no sin.