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Okay--If anyone else has this problem, here is what I did.
I started with the obvious screens. Things like index.php user.php etc. Any screen that I knew was not an include. I added the #!/usr/bin/php line to those files. Then, I went to every single link on the site, and if I got an error, I went to the file and added the missing line.
Did I miss some? Probably, but I will find them eventually.
Did I change some that I shouldn't have? Yes--and, when I did the #!/usr/bin/php line showed up on the top of the page (and kind of screwed up the theme). In this case you have to figure out which file you changed, but shouldn't have, and then delete the line.
Was it the best method? No, but it got me up and running.
It will also make upgrading a drag (I suspect), but them's the breaks if I want to use XOOPS at this location.
O