Thanks to Adobe for keeping this post up here. Even 4 years later, it offered a solution for my similar issue.
However, the part of 'click in the empty frames one page at a time' would be painfully slow with a large document. My answer was similar though:
- Run the multi-page import
- Create a new master and place my desired PDF on the B master in the correct position/orientation.
- Run the cdflash script to add a page after each existing page; this asks which Master to use, specify the B master and let it run.