You are correct, the DX VF-1 missiles will be too large for the VF-31.  Also, the connectors are complete different.  The closest compatible set of missiles come from the DX - YF-19 Full Set and those attachments are compatible with the VF-31.  Keep in mind that the Super Parts for the VF-31 covers the attachment points for the missiles so you will need the special shield adaptor in order to attach the missiles with the Super parts.