Hi Bill,
Yep, was able to get this working.
Multisite added the following line to my .htaccess:
RewriteRule ^(.*\.php)$ $1 [L]
Commented that out and 404's are working on the primary domain again.
Not entirely sure what the purpose of that line is, but everything appears to be working correctly without it. I think it's designed to remove the file extension.
Other than that hiccup - all is well with your plugin.
Thanks!
CB