Hey James
Currently for us non-root user there may be a way
but i havnt found it yet, but I can help with changing default system tones
1) Create a folder on your SD Card using 'Astro file manager' or any software that allows you to view SD Card contents called Audio
2) In folder create 3 sub-folders notifications, alarms, ringtones
3) Put your desired tones into the various folders,
so if you want a different timer tone, place it in alarms.
4) Change your timer and your done
Hope ive helped
Kid_android