1. I'm a little confused by what you said, the double entry is not enough? you enter Shenzhen for one entry, then return to Shenzhen from Hong Kong is another entry. if you want to get the multiple entry visa, you should prepare the documents to certify that you need the multiple entries, such as your itinerary
2. if you apply for multiple entry visa valid for hald a year at Chinese embassy in Singapore, you should pay 150 Singaporean dollars.
3. You don't need to apply for Hong Kong visa because Malaysian paspsort holders are exempt from a visa to Hong Kong for up to 90 days.