Spouse visa

Dear all,
I have been to Japan last year in July as a tourist from July 1 to sept 23/2015.
This year I applied at Japanese language school and I have been granted the certificate of eligibility but the Japanese Embassy in my country (Ethiopia) Said my Japanese language skill is not up to the required level and that they can not decided about the issuance of my visa unless they consult the the head office. My documents sent back to the immigration in Japan after waiting for over one month my result came out and my students visa refused. They also put a stamp on the back of my passport as well. I have changed my passport now because I did want to have the stamp on my passport and also my birth year was not correct so I had to correct it.

I am marrying my Japanese girlfriend this month (she lives in my country and she is leaving end of September to Japan). she is going to apply for the COE in japan and we are planning to request spouse visa.
My question is:
---Could the previous denial of student visa by the immigration makes my spouse visa request rejected or COE rejected? I am very worried about these. And if I am Granted the COE, Is the embassy in my country issue the spouse visa right away or send it back to the head office in Japan again? What are our chances?

Thank you very much in advance

If your marriage is correct, then there will be no problem.
Failing to get a student visa doesn't affect your marriage visa request in anyway.

The problem is that documents you give to the immigration office should confirm that your marriage is not fake.
You may be required to state time you met your wife and how many times did she visit your country. If it's only one time, that would be a problem.

Thank you very much for getting back to me!
She lived in my Country for nearly two years. She has been working as a Jica volunteer and her contract will be over end of this month. Our marriage is not fake at all. She has also met my parents. Sinc she lived here for a while her mother is the one going to be my sponsor so there is no problem or lie in our marriage. Thank you very much for your uplifting vomment.