Please give read/write access to /tmp file system to <sid>adm user, it will take care own its own all temp files.
When your will stop SAP and execute cleanipc command successfully with <sidadm> all files which are not required should be removed. For java fifo files, as said before, they can be removed any time but not at system start up, same applies for other files generated at the time of startup.
Regards,
Divyanshu