Nice project and nice web page you have set up there. I especially like the reusing of common materials (bike frames) as it fits so well with the spirit and budget of most hobbyist.
Two points:
You mention here and on your site you are using the Mega128 chip, however I think you mean the Mega1280 chip as used on the orginal Arduino mega board. There is a Mega128 chip and is used in a board by the open source wiring project, however the Mega128 chip is not directly supported by the Arduino IDE without modification to some of the files.
Nice that you found out one of the universal laws of pratical electronics: The semiconductor(s) will always fail first to protect any fuse used in the system.
Lefty