Hi maiohwmai,
I just wanted to notify that I used "350d_bootflag_update_20090914.zip" from your first post, everything seemed to went well, but after restarting my camera it would not poweron. I pressed shutter release and it powered on but I could not get into menus, take pictures or power down.
I removed the battery and used another CF and the second file (bootflag-20090921.zip). When powering on again I got the blue and red led flashing, I put back the bootable CF and got the 3200 ISO and STDOUT.TXT file. Camera is working well again.
So the second file seems to work better for me.
Thank you for your work !