My USB port as just died so need to return it to Nokia for repair. I have modded the device a little (LED's, boot up, some icons). Does this affect warranty? Should I revert everything back to default?

Take a backup of your system (including customizations, make a note of everything) and then restore to default before returning it, that way your not giving the Nokia repair engineer anything to consider, they may think you started modding it hardware wise just because of a few software mods.

But thats my opinion from a 2nd/3rd line IT perspective.