I'm going to fill this in just in case somebody in Googleland ends up here.
I ended up creating a new instance of Mysql with a new ibdata1 and log files. Then stopped the service and replaced the new ibdata1 file with the old one. I also changed the my.ini file to force a recovery. Then I restarted the mysql service. While the old data was accessed, websites would not respond.
So first I used Mysql Browser to make sure the information was visible in the tables. Then I created a dump via the command line and mysqldump. Next I uninstalled the instance of Mysql and created a new one. Went back to the command line and imported the dump.
The users were brought over because that information is MyIsamm and I had those files. The dump carried the data over.
The actual file recovery must have damaged some information as I had to manually shift through the ibdata1 file for some table data, but at the end of the day everything was put back where it belongs.
I now will create a dump file every evening for backup.
The End.