1.) No set bonus is definitely gone
2.) If the original shell was empty of mods before the update it will be filled with 258s. However, for players that kept their 252 armoring,mods and enhancements in the 258 shells, will NOT have been refilled with 258s. I did that for a lot of my toons so i'm missing a lot of 258 armorings with set bonus.
3.) No. Tooltip didn't change.