I feel your pain since the instruction didn't state anything of a sort about this "vars" file. But anyhow, I have upgraded from 5.47d to 6.04 and at one point I didn't any of my forums.

This was after rebuilding the boards. So had to do the whole process again. But I do recall from the other server I was upgrading the board that I did in fact, overwrote that file and I clicked on the UBB5 upgrade and it worked. It seemed to me that it's looking for the date.pl file when I moved the board over to another server.
JD