Visa problem

I am Husnul Abrar from Malaysia. I arrived in Turkey on 7/6/2022. I study in a madrasa in Istanbul. on 5/9/2022 I left Turkiye through the Kapikule-Bulgarian border. 2 days before the end of 3 months. when i re-entered turkiye, the immigration gave me 10 days to apply for a visa because i gave them a letter of offer to study at the university. from Istanbul, I went straight to I?d?r to manage the student certificate. At the same time, I tried to apply for a visa online, but was unsuccessful. i went to the immigration office in i?d?r on 20/9/2022 but they didn't accept me because i was 2 days late. I got a student certificate from the university on 22/9/2022. they told me to contact the consulate. i have contacted the malaysia embassy in ankara, but they said that they can't help because this problem can only be solved by immigration. I have gone to the Turkish-Iranian border in Gürbulak to pay the fine and re-entered Turkey without success. i have also been to the turkish - georgian border in akta?. they told me to get a letter of support from the immigration office.
i went to the immigration office and they told me to leave turkey for 3 months or apply for a visa from the turkish consulate in the country i entered.
my questions:
1) can I apply for a visa to re-enter Turkey because I have got a student certificate from the university
2) if possible, what documents do I need to prepare before applying for a visa ?
3) how much is the fee?

thank you very much for your answer