Malaysian passport holder with Permanent Residency in Japan-can I apply for visa myself?

I will be going to Hong Kong in October to join up with friends, leaving the next day for Shenzen to fly to Ningbo, then to Shanghai & Changsha before returning to Hong Kong for my flight back to Japan.

My friends in HK will be making all travel arrangements to & in China but I will book my own ticket from Japan to HK.
1. Can I apply for visa myself in Tokyo Embassy?
2. Given the above itinerary, what documents do I need? Thank you.
Carol M