It would appear that you overwrote everything on your drive. Did you have a separate partition on your main hard drive that was mounted in Windows as drive D:
? If so it would appear that it is gone.
If you have that partition backed up, this will help you restore your files.
Boot into your Ubuntu install CD and repartition your drive to include a data partition that you can mount in Ubuntu.
Format the partition to either ext3 or ext4 and make it as large as you like.
Reboot so you boot from your internal hard drive and plug in your drive with the backup and copy all the files to the new partition you just created.
I'm not sure what you want to know about the initrd.img
file, but reading the Wikipedia entry might put your mind at ease. I don't think its your problem.
Your system is just two partitions. One large partition that is your Ubuntu OS, and a small boot partition needed to boot Ubuntu. If you didn't back up your data you are out of luck. If its backed up just restore it by following the instructions above, or a myriad of others on the web.