We were liveaboards and found that having a full enclosure was indispensable. To specifically answer your questions:
1) Go with a lot of glass - it's not just light and visibility, but also solar/thermal performance.
2) Our winds are all fixed. While I've thought it would be nice to have zip out windows with screens, I can't imagine keeping track of all of the pieces.
3) We don't have cloth coverings and can't say that we have ever really felt the need
Just make sure you consider winch handle clearance, running rigging clearance, rail mounted items such as BBQ's, backstay or transom access, etc. when building a full enclosure. Our enclosure is comprised of the following sections:
1) Bimini (top)
2) Bimini (right side, left side, and two rear panels)
4) Connector between Bimini and Dodger
5) "Zip up doors" on left and right of connector to allow cockpit access.
All pieces except for the dodger top and the bimini top are mostly glass with fabric edging. If you zoom into the picture below you can see it better.