Denied file read access on file I own and have full r/w permissions on
From debugging a different problem (which showed up as deny file-read-data in the Console, see the other answer), it seems that sandboxd prevents sandboxed applications from reading quarantined data, so I think you'd need to remove the attribute with:

xattr -d com.apple.quarantine /path/to/file

(see for instance https://superuser.com/a/28394/46794). You'd need to prefix the command with sudo if the file didn't belong to your user, but according to your info it does.

The other user reported that using a non-sandboxed application fixed the problem, and this would confirm that sandboxing is at fault.

An aside: When ls reports extended attributes with @ next to the permission field, you don't need ls -le file, but instead ls -l@ file.