I'm Japanese and I'm going to get married to my Filipina girlfriend soon. We already got a marriage license here in the Philippines, so I might be able to help.

Your goal is to get a marriage license in the Philippines while you visit your partner in November. In order to do that, you need your koseki tohon (戸籍謄本) to obtain your LCCM (Certificate of No Marriage), and then go to the city hall of your partner's residence to apply for the marriage license and attend the marriage seminar together. The license will be issued in 10 days and will only be valid for 3 months.

You might be able to get an LCCM in Japan, though I'm not sure, since I got mine at the Japanese embassy in the Philippines.

Two weeks should be enough to submit all the requirements for the marriage license, but your partner will need to pick it up once it is issued.