What a action packed and informative write up. You sparked ideas that I didn't even know were considerations when running in multisite mode. What brought me here was my quest to create a custom wp-signup.php without messing with the core. Mine's currently modified to the teeth and I'd like to resolve this before my next core upgrade (yikes). The script you shared to block access to wp-signup.php sounds great as it seems to help kill two birds with one stone. I can have my alternate signup and divert some splog attempts. However, how would someone address the "register" link presented in wp-login.php? When used, wp-login.php redirects to wp-signup.php if multisite is enabled. Any thoughts would be appreciated.

Have a great day!