4 (simple) issues / Multisite / directory structured

Cheers! Thank you for your assistance and for a GREAT community :slight_smile:
I recently started using Multisite, It's great but I can't decide on the best solution regarding:

1.Purchased a SSL, installed it, ran HTTPS for WP plugin fixed my pages still...it breaks on the (test, empty, using twenty themes) network sites. How can I disable it for my network sites, or make it work? Or it does work but breaks my theme, can be observed at https://aesconsortium.com/test1/

2.The WPMU plugin manager displays only 4 plugins from the many that I have, all are Network enabled but shows only 4. How can I control which site/user controls which plugins? Should I install them in each site, individually?

3.What plugin should I use in order to offer visitors a way to register using their (confirmed) e-mail? Also how to make a pop-up Login/Register similar to gigaom.com? Login in a pop-up not a separate page...

4.Themes, TwentyTwelve for ex. don't work at all times, how could I detect a possible conflict in plugins or... what could cause this to happen?

Thank you, I appreciate your answer as I'm not the only one dealing with noob problems such these. Any simple answer would help a great deal!
Thanks!