How can I rename a footage .ai file for AE without breaking the references?
Save the project in XML file format, do as you already did, open it in a text editor, find-replace the name. Open the modified file in AE and re-save it in its normal binary format (aep).

Size shouldn't be an issue since renaming a file doesn't change it size. It seems like you have edited the aep file? Hope this helps!

More on the topic here:
http://help.adobe.com/en_US/aftereffects/cs/using/WS3878526689cb91655866c1103906c6dea-7fa0a.html